The half-life of 227Th by direct and indirect measurements

International Nuclear Information System (INIS)

Collins, S.M.; Pommé, S.; Jerome, S.M.; Ferreira, K.M.; Regan, P.H.; Pearce, A.K.

2015-01-01

Utilising a chemically purified solution the radioactive half-life of 227 Th has been determined indirectly by observation of the ingrowth of 223 Ra using an ionisation chamber (IC) and for the first time by direct observation of the change in activity with time using a high-purity germanium (HPGe) γ-ray spectrometer. The radioactive decay was observed for ~104 days (~5.6 half-lives) by γ-ray spectrometry and approximately 63 days and 72 days (~3.4 and ~3.9 half-lives) using an ionisation chamber (IC). The resulting half-life values – 18.695 (4) days (IC) and 18.683 (20) days (HPGe) – are consistent and detailed uncertainty budgets are presented for the two measurement techniques. A weighted mean of our results of 18.695 (4) days is inconsistent with the most precise published half-life value of 18.7176 (52) days (Jordan and Blanke, 1967). A critical evaluation of literature data has been performed, indicating a paucity of reliable and independent measurements. Selected independent published values have been used to determine a recommended half-life of 18.697 (7) days. A method has been introduced in the course of this work so that the recommended half-life of 227 Th as determined by ingrowth can be modified if a different 223 Ra half-life has been determined, evaluated and adopted. - Highlights: • First direct measurement of 227 Th half-life by HPGe γ-ray spectrometry. • Precision half-life measurement by ionisation chamber. • New half-life of 18.695 (4) days determined. • Critical evaluation of published half-lives and recommended value determined

Experimental half-life determination of 176Lu

International Nuclear Information System (INIS)

Kossert, Karsten; Jörg, Gerhard; Gostomski, Christoph Lierse v.

2013-01-01

The half-life of the naturally occurring long-lived rare earth isotope 176 Lu was determined by a combination of highly sophisticated experimental procedures in order to further improve the reliability and the precision of literature data. The amount of lutetium in the samples was determined by inductively coupled plasma optical emission spectrometry (ICP-OES) using a NIST reference standard. The isotopic ratio N( 176 Lu)/N(Lu) in the samples was measured by means of inductively coupled plasma high resolution mass spectrometry (ICP-HRMS). The activity divided by the mass of Lu was determined by applying liquid scintillation (LS) counting. The LS counting efficiency of the beta/gamma emitter 176 Lu was determined with the CIEMAT/NIST efficiency tracing technique with low uncertainty. The influences of colour quenching and background effects are discussed in this paper. The half-life was found to be 3.640(35)×10 10 y. The result is in good agreement with other evaluations and the relative standard uncertainty of 0.95% is among the lowest of previously published data. - Highlights: • The half-life of 176 Lu was determined by ICP-OES, ICP-HRMS and LSC. • The LSC efficiency was determined with the CIEMAT/NIST method. • The half-life was found to be 3.640(35)×10 10 y

Measurement of the 230U half-life

International Nuclear Information System (INIS)

Pommé, S.; Altzitzoglou, T.; Van Ammel, R.; Suliman, G.; Marouli, M.; Jobbágy, V.; Paepen, J.; Stroh, H.; Apostolidis, C.; Abbas, K.; Morgenstern, A.

2012-01-01

The 230 U half-life was determined by measuring the decay curve of 230 U sources by various nuclear detection techniques: α-particle counting at a defined small solid angle; 4πα+β counting with a windowless CsI sandwich spectrometer, a liquid scintillation counter and a pressurised proportional counter; gamma-ray spectrometry with a HPGe detector and nearly-2π α-particle counting with an ion-implanted silicon detector. Depending on the technique, the decay was followed for 100–200 d, which is 5–10 times the 230 U half-life. The measurement results of the various techniques were in good mutual agreement. The mean value, T 1/2 ( 230 U)=20.23 (2) d, is lower than the literature value which is based on one measurement in 1948 and resulted in a half-life value of 20.8 d without statement of uncertainty. A correction for the ingrowth of the long-lived 210 Pb and its daughter products may have been overlooked in the past. - Highlights: ► Half-life of 230 U determined by various nuclear detection techniques. ► Result T 1/2 ( 230 U)=20.23 (2) d is lower than the literature value. ► 230 U/ 226 Th decay series has potential use in alpha-immunotherapy.

Half-life of Xe120

Science.gov (United States)

Phillips, A. A.; Andreoiu, C.; Ball, G. C.; Bandyopadhyay, D.; Behr, J. A.; Chupp, T. E.; Finlay, P.; Garrett, P. E.; Grinyer, G. F.; Hackman, G.; Hayden, M. E.; Hyland, B.; Nuss-Warren, S. R.; Pearson, M. R.; Schumaker, M. A.; Smith, M. B.; Svensson, C. E.; Tardiff, E. R.; Valiente-Dobón, J. J.; Warner, T.

2006-08-01

We have measured the half-life of Xe120 using a high-purity germanium (HPGe) detector to monitor the 176, 178, and 762 keV γ rays from Xe120 β+ decay. The result, 46±0.6 min, differs significantly from the value 40±1 min reported by Andersson [Ark. Fys. 28, 37 (1964)]. We have also measured the half-lives of Cs120 and I120 to be 60±0.7 s and 82.1±0.6 min, respectively, both of which are consistent with previous measurements.

A new determination of the 209Po half-life

International Nuclear Information System (INIS)

Collé, R; Fitzgerald, R P; Laureano–Perez, L

2014-01-01

A substantial 25% error in the then-known and accepted (102 ± 5) year half-life of 209 Po was reported on in 2007. This error was detected from decay data from two separate primary standardizations of a 209 Po solution standard, which were performed approximately 12 years apart. Despite author claims that this observation was not a new half-life determination, it was nevertheless included in subsequent nuclear data evaluations and compilations to obtain a currently tabulated value of (115 ± 13) a, computed from the median and range of the two half-life reports. A third primary standardization on the identical 209 Po solution has since been performed to derive a new half-life value of (125.2 ± 3.3) a. This half-life determination was obtained from 30 distinct data sets over a period of 20.7 years, encompassing over 700 liquid scintillation measurements with nearly 50 counting sources all prepared from the same solution, and as obtained over a very broad range of measurement conditions (composition of cocktails, characteristics of counters, time sequencing) during five periods in 1993, 1994, 2005, and 2013. (paper)

Measurement of the 20F half-life

Science.gov (United States)

Hughes, M.; George, E. A.; Naviliat-Cuncic, O.; Voytas, P. A.; Chandavar, S.; Gade, A.; Huyan, X.; Liddick, S. N.; Minamisono, K.; Paulauskas, S. V.; Weisshaar, D.

2018-05-01

The half-life of the 20F ground state was measured using a radioactive beam implanted in a plastic scintillator and recording β γ coincidences together with four CsI(Na) detectors. The result, T1 /2=11.0011 (69) stat(30) sys s, is at variance by 17 combined standard deviations with the two most precise results. The present value revives the poor consistency of results for this half-life and calls for a new measurement, with a technique having different sources of systematic effects, to clarify the discrepancy.

Precise half-life measurement of the superallowed emitter 30S

Science.gov (United States)

Iacob, V. E.; Hardy, J. C.; Chen, L.; Horvat, V.; Bencomo, M.; Nica, N.; Park, H. I.; Roeder, B. T.; Saastamoinen, A.

2018-03-01

We have measured the half-life of 30S, the parent of a superallowed 0+→0+β transition, to a high precision using very pure sources and a 4 π proportional gas counter to detect the decay positrons. Our result for the half-life is 1.179 92(34) s. As a by-product of this measurement, we determine the half-life of its daughter, 30P, to be 2.501(2) min.

Beryllium-10: Half-life and AMS-standards

International Nuclear Information System (INIS)

Hofmann, H.J.; Beer, J.; Bonani, G.; von Gunten, H.R.; Raman, S.; Suter, M.; Walker, R.L.; Woelfli, W.; Zimmermann, D.

1987-01-01

Absolute AMS measurements of 10 Be require reliable standards for calibration. Among the existing standards, rather large differences have been observed. These differences were found partially to be due to the different half-life values which were assumed. Also for comparison of AMS data with activity measurements, it is necessary to know the 10 Be half-life as precisely as possible. Starting with 5 ml of the standardized ORNL-MASTER solution, a working solution with a well-defined 10 Be content was prepared. Its specific activity was determined by liquid scintillation counting. This measurement yielded a new value of (1.52 +- 0.05) My for the 10 Be half-life, which is in agreement with the previously reported values but is about three times more accurate. Two independent dilution series produced new AMS standards with 10 Be/ 9 Be ratios of the order of 10 -10 and 10 -11 . These standards were measured at the ETH/SIN AMS facility with high accuracy and are compared with other available 10 Be standards. 15 refs, 2 figs., 3 tabs

Experimental study of half-life determinations using 60Co

International Nuclear Information System (INIS)

Rutledge, A.R.; Smith, L.V.; Merritt, J.S.

1983-01-01

The half-life of 60 Co was determined by two methods, (i) the 4π#betta# ionization chamber method and (ii) the 4π #betta#-#betta# coincidence method. The first is a relative counting method in which the only rate-dependent correction is for background, whereas the second is an 'absolute' counting method which involves several rate-dependent corrections. In addition, various methods of calculation of the results were tested. The half-life values for the two counting systems were in good agreement and the weighted mean value for the half-life of 60 Co was found to be 1925.02+-0.47 d. (orig.)

Determination of plutonium-241 half-life by mass spectrometric measurement

International Nuclear Information System (INIS)

Hiyama, Takashi; Wada, Yukio; Onishi, Koichi

1982-01-01

Much data for Pu-241 half-life have been reported, but these values range from 13.8 years to 15.1 years depending on investigators. In order to define the half-life of Pu-241, the half-life was calculated by analyzing the mass spectrometry data obtained in the author's laboratory over the past six years on Plutonium Isotopic Standard Reference Materials prepared at the National Bureau of Standards (NBS). The sample used for this work consisted of SRM-947 and SRM-948 prepared at NBS. Before mass spectrometric analysis, the plutonium aliquot was separated from its Am-241 daughter by anion exchange chromatography, since Am-241 is not distinguished from Pu-241 in the mass spectrometer. 241 Pu/ 239 Pu and 241 Pu/ 240 Pu ratios were calculated from the values of mass spectrometric measurement. From the relation of log N to time, the half-life of Pu-241 was determined, based on the slope using a least squares fit. The half-life of Pu-241 was estimated to be 14.29+-0.15 years. (Yoshitake, I.)

Half-life evaluations for 3H, 90Sr, and 90Y

International Nuclear Information System (INIS)

MacMahon, Desmond

2006-01-01

A recent paper has reviewed methods for the evaluation of discrepant sets of data and demonstrated the results of applying these methods to the published half-life data of 90 Sr and 137 Cs [MacMahon, T.D., Pearce, A., Harris, P., 2004. Convergence of techniques for the evaluation of discrepant data. Appl. Radiat. Isot. 60, 275-281]. The half-life data for 3 H has been subject to a comprehensive review and critical evaluation by Lucas and Unterweger [2000. Comprehensive review and critical evaluation of the half-life of tritium. J. Res. Natl. Inst. Stand. Technol. 105, 541-549]. The current paper reports the results of applying the various evaluation procedures of MacMahon et al. Convergence of techniques for the evaluation of discrepant data. Appl. Radiat. Isot. 60, 275-281] to the data of Lucas and Unterweger [Comprehensive review and critical evaluation of the half-life of tritium. J. Res. Natl. Inst. Stand. Technol. 105, 541-549], resulting in a recommended half-life of 4497(4) days. MacMahon et al. [Convergence of techniques for the evaluation of discrepant data. Appl. Radiat. Isot. 60, 275-281] highlighted problems in the evaluation of the discrepant half-life data of 90 Sr, in particular the worrying upward trend in the data, where the weighted mean of all the measurements increases, on average, by 35 days each time a new measurement result is added. The current paper reports on further analyses of these data. New measurements of the half-life of 90 Y have been reported by Kossert and Schrader [2004. Standardization by liquid scintillation counting and half-life measurements of 90 Y. Appl. Radiat. Isot. 60, 741]. This has prompted a new evaluation of all available published 90 Y half-life data. The data are fairly consistent, and a value of 64.063(16) h is recommended

Half-life of the superallowed β+ emitter Ne18

Science.gov (United States)

Grinyer, G. F.; Smith, M. B.; Andreoiu, C.; Andreyev, A. N.; Ball, G. C.; Bricault, P.; Chakrawarthy, R. S.; Daoud, J. J.; Finlay, P.; Garrett, P. E.; Hackman, G.; Hyland, B.; Leslie, J. R.; Morton, A. C.; Pearson, C. J.; Phillips, A. A.; Schumaker, M. A.; Svensson, C. E.; Valiente-Dobón, J. J.; Williams, S. J.; Zganjar, E. F.

2007-08-01

The half-life of Ne18 has been determined by detecting 1042-keV γ rays in the daughter F18 following the superallowed-Fermi β+ decay of samples implanted at the center of the 8πγ-ray spectrometer, a spherical array of 20 HPGe detectors. Radioactive Ne18 beams were produced on-line, mass-separated, and ionized using an electron-cyclotron-resonance ionization source at the ISAC facility at TRIUMF in Vancouver, Canada. This is the first high-precision half-life measurement of a superallowed Fermi β decay to utilize both a large-scale HPGe spectrometer and the isotope separation on-line technique. The half-life of Ne18, 1.6656 ± 0.0019 s, deduced following a 1.4σ correction for detector pulse pile-up, is four times more precise than the previous world average. As part of an investigation into potential systematic effects, the half-life of the heavier isotope Ne23 was determined to be 37.11 ± 0.06 s, a factor of 2 improvement over the previous precision.

Measurement of the half-life of 68Ga

International Nuclear Information System (INIS)

García-Toraño, Eduardo; Peyrés Medina, Virginia; Romero, Eduardo; Roteta, Miguel

2014-01-01

The half-life of the positron-emitter 68 Ga has been measured by following the decay rate with two systems based on ionization chamber and Ge detectors. The decay rate was measured for periods of time up to 10 half-lives. The combination of the 6 results obtained with both systems gives a value of T 1/2 =67.845(18) min, in good agreement with recommended data and with an uncertainty lower than any other previously reported value. - Highlights: • The half-life of the positron-emitter radionuclide 68 Ga was measured. • Two measurement setups (ionization chamber and Ge detector) were used. • Results agree with evaluated data but exhibit lower uncertainty

Half-life predictions for decay modes of superheavy nuclei

International Nuclear Information System (INIS)

Duarte, S.B.; Tavares, O.A.P.; Goncalves, M.; Rodriguez, O.; Guzman, F.; Barbosa, T.N.; Garcia, F.; Dimarco, A.

2004-09-01

We applied the Effective Liquid Drop Model (ELDM) to predict the alpha-decay, cluster emission and cold fission half-life-values of nuclei in the region of Superheavy Elements (SHE). The present calculations have been made in the region of the ZN-plane defined by 155 <=N <=220 and 110<=Z<=135. Shell effects are included via the Q-value of the corresponding decay case. We report the results of a systematic calculation of the half-life for the three nuclear decay modes in a region of the ZN-plane where superheavy elements are expected to be found. Results have shown that, among the decay modes investigated here, the alpha decay is the dominant one. i.e, the decay mode of smallest half-lives. Half-life predictions for alpha decay, cluster emission and cold fission for the isotopic family of the most recent SHE detected of Z=115 and for the isotopic family of the already consolidated SHE of Z=111 are presented. (author)

Intrinsically disordered segments and the evolution of protein half-life

Science.gov (United States)

Babu, M.

2013-03-01

Precise turnover of proteins is essential for cellular homeostasis and is primarily mediated by the proteasome. Thus, a fundamental question is: What features make a protein an efficient substrate for degradation? Here I will present results that proteins with a long terminal disordered segment or internal disordered segments have a significantly shorter half-life in yeast. This relationship appears to be evolutionarily conserved in mouse and human. Furthermore, upon gene duplication, divergence in the length of terminal disorder or variation in the number of internal disordered segments results in significant alteration of the half-life of yeast paralogs. Many proteins that exhibit such changes participate in signaling, where altered protein half-life will likely influence their activity. We suggest that variation in the length and number of disordered segments could serve as a remarkably simple means to evolve protein half-life and may serve as an underappreciated source of genetic variation with important phenotypic consequences. MMB acknowledges the Medical Research Council for funding his research program.

Designing of peptides with desired half-life in intestine-like environment

KAUST Repository

Sharma, Arun

2014-08-20

Background: In past, a number of peptides have been reported to possess highly diverse properties ranging from cell penetrating, tumor homing, anticancer, anti-hypertensive, antiviral to antimicrobials. Owing to their excellent specificity, low-toxicity, rich chemical diversity and availability from natural sources, FDA has successfully approved a number of peptide-based drugs and several are in various stages of drug development. Though peptides are proven good drug candidates, their usage is still hindered mainly because of their high susceptibility towards proteases degradation. We have developed an in silico method to predict the half-life of peptides in intestine-like environment and to design better peptides having optimized physicochemical properties and half-life.Results: In this study, we have used 10mer (HL10) and 16mer (HL16) peptides dataset to develop prediction models for peptide half-life in intestine-like environment. First, SVM based models were developed on HL10 dataset which achieved maximum correlation R/R2 of 0.57/0.32, 0.68/0.46, and 0.69/0.47 using amino acid, dipeptide and tripeptide composition, respectively. Secondly, models developed on HL16 dataset showed maximum R/R2 of 0.91/0.82, 0.90/0.39, and 0.90/0.31 using amino acid, dipeptide and tripeptide composition, respectively. Furthermore, models that were developed on selected features, achieved a correlation (R) of 0.70 and 0.98 on HL10 and HL16 dataset, respectively. Preliminary analysis suggests the role of charged residue and amino acid size in peptide half-life/stability. Based on above models, we have developed a web server named HLP (Half Life Prediction), for predicting and designing peptides with desired half-life. The web server provides three facilities; i) half-life prediction, ii) physicochemical properties calculation and iii) designing mutant peptides.Conclusion: In summary, this study describes a web server \\'HLP\\' that has been developed for assisting scientific

On the 209Po half-life error and its confirmation. A critique

International Nuclear Information System (INIS)

Colle, R.; Colle, A.M.

2016-01-01

A recent report on 209 Po claimed to have made a determination of the 125-a half-life from measurements made over 0.8 % of one half-life. A careful reanalysis of the original data with a more complete and rigorous consideration of the underlying uncertainties demonstrates that this claim cannot withstand critical scrutiny. More importantly, this critique examines the larger issue as to what constitutes a valid half-life determination, and highlights that a careful and realistic analysis beyond the mere fitting of decay data to an exponential function is required for the measurement and reporting of half-life values. (author)

Determination of the {sup 151}Sm half-life

Energy Technology Data Exchange (ETDEWEB)

Be, Marie-Martine; Cassette, Philippe [CEA, LIST, Gif sur Yvette (France). LNE-Laboratoire National Henri Becquerel; Isnard, Helene [CEA-LANIE, Gif sur Yvette (France); and others

2015-07-01

New measurements have been undertaken to determine the half-life of {sup 151}Sm. A pure {sup 151}Sm solution was obtained after chemical separation from a samarium solution resulting from the dissolution of an irradiated samarium sample. The concentration of {sup 151}Sm in the solution was measured by mass spectrometry, combined with the isotope dilution technique. The activity of the solution was measured by liquid scintillation counting by six European laboratories as part of an international comparison. These combined results lead to a half-life of T{sub 1/2} = 94.6(6)a.

High-precision half-life determination for the superallowed β+ emitter Ga62

Science.gov (United States)

Grinyer, G. F.; Finlay, P.; Svensson, C. E.; Ball, G. C.; Leslie, J. R.; Austin, R. A. E.; Bandyopadhyay, D.; Chaffey, A.; Chakrawarthy, R. S.; Garrett, P. E.; Hackman, G.; Hyland, B.; Kanungo, R.; Leach, K. G.; Mattoon, C. M.; Morton, A. C.; Pearson, C. J.; Phillips, A. A.; Ressler, J. J.; Sarazin, F.; Savajols, H.; Schumaker, M. A.; Wong, J.

2008-01-01

The half-life of the superallowed β+ emitter Ga62 has been measured at TRIUMF's Isotope Separator and Accelerator facility using a fast-tape-transport system and 4π continuous-flow gas proportional counter to detect the positrons from the decay of Ga62 to the daughter Zn62. The result, T1/2=116.100±0.025 ms, represents the most precise measurement to date (0.022%) for any superallowed β-decay half-life. When combined with six previous measurements of the Ga62 half-life, a new world average of T1/2=116.121±0.021 ms is obtained. This new half-life measurement results in a 20% improvement in the precision of the Ga62 superallowed ft value while reducing its mean by 0.9σ to ft=3074.3(12) s. The impact of this half-life measurement on precision tests of the CVC hypothesis and isospin symmetry breaking corrections for A⩾62 superallowed decays is discussed.

Precision half-life measurement of 17F

Science.gov (United States)

Brodeur, M.; Nicoloff, C.; Ahn, T.; Allen, J.; Bardayan, D. W.; Becchetti, F. D.; Gupta, Y. K.; Hall, M. R.; Hall, O.; Hu, J.; Kelly, J. M.; Kolata, J. J.; Long, J.; O'Malley, P.; Schultz, B. E.

2016-02-01

Background: The precise determination of f t values for superallowed mixed transitions between mirror nuclide are gaining attention as they could provide an avenue to test the theoretical corrections used to extract the Vu d matrix element from superallowed pure Fermi transitions. The 17F decay is particularly interesting as it proceeds completely to the ground state of 17O, removing the need for branching ratio measurements. The dominant uncertainty on the f t value of the 17F mirror transition stems from a number of conflicting half-life measurements. Purpose: A precision half-life measurement of 17F was performed and compared to previous results. Methods: The life-time was determined from the β counting of implanted 17F on a Ta foil that was removed from the beam for counting. The 17F beam was produced by transfers reaction and separated by the TwinSol facility of the Nuclear Science Laboratory of the University of Notre Dame. Results: The measured value of t1/2 new=64.402 (42) s is in agreement with several past measurements and represents one of the most precise measurements to date. In anticipation of future measurements of the correlation parameters for the decay and using the new world average t1/2 world=64.398 (61) s, we present a new estimate of the mixing ratio ρ for the mixed transition as well as the correlation parameters based on assuming Standard Model validity. Conclusions: The relative uncertainty on the new world average for the half-life is dominated by the large χ2=31 of the existing measurements. More precision measurements with different systematics are needed to remedy to the situation.

The proteomic complexity and rise of the primordial ancestor of diversified life

Directory of Open Access Journals (Sweden)

Kim Kyung

2011-05-01

Full Text Available Abstract Background The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. This urancestor accumulated genetic information before the rise of organismal lineages and is considered to be either a simple 'progenote' organism with a rudimentary translational apparatus or a more complex 'cenancestor' with almost all essential biological processes. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content. However, most of these studies were based on molecular sequences, which are fast evolving and of limited value for deep evolutionary explorations. Results Here we engage in a phylogenomic study of protein domain structure in the proteomes of 420 free-living fully sequenced organisms. Domains were defined at the highly conserved fold superfamily (FSF level of structural classification and an iterative phylogenomic approach was used to reconstruct max_set and min_set FSF repertoires as upper and lower bounds of the urancestral proteome. While the functional make up of the urancestral sets was complex, they represent only 5-11% of the 1,420 FSFs of extant proteomes and their make up and reuse was at least 5 and 3 times smaller than proteomes of free-living organisms, repectively. Trees of proteomes reconstructed directly from FSFs or from molecular functions, which included the max_set and min_set as articial taxa, showed that urancestors were always placed at their base and rooted the tree of life in Archaea. Finally, a molecular clock of FSFs suggests the min_set reflects urancestral genetic make up more reliably and confirms diversified life emerged about 2.9 billion years ago during the start of planet oxygenation. Conclusions The minimum urancestral FSF set reveals the urancestor had advanced metabolic capabilities, was especially rich in nucleotide metabolism enzymes, had pathways for the

Personalized medicine beyond genomics: alternative futures in big data-proteomics, environtome and the social proteome.

Science.gov (United States)

Özdemir, Vural; Dove, Edward S; Gürsoy, Ulvi K; Şardaş, Semra; Yıldırım, Arif; Yılmaz, Şenay Görücü; Ömer Barlas, I; Güngör, Kıvanç; Mete, Alper; Srivastava, Sanjeeva

2017-01-01

No field in science and medicine today remains untouched by Big Data, and psychiatry is no exception. Proteomics is a Big Data technology and a next generation biomarker, supporting novel system diagnostics and therapeutics in psychiatry. Proteomics technology is, in fact, much older than genomics and dates to the 1970s, well before the launch of the international Human Genome Project. While the genome has long been framed as the master or "elite" executive molecule in cell biology, the proteome by contrast is humble. Yet the proteome is critical for life-it ensures the daily functioning of cells and whole organisms. In short, proteins are the blue-collar workers of biology, the down-to-earth molecules that we cannot live without. Since 2010, proteomics has found renewed meaning and international attention with the launch of the Human Proteome Project and the growing interest in Big Data technologies such as proteomics. This article presents an interdisciplinary technology foresight analysis and conceptualizes the terms "environtome" and "social proteome". We define "environtome" as the entire complement of elements external to the human host, from microbiome, ambient temperature and weather conditions to government innovation policies, stock market dynamics, human values, political power and social norms that collectively shape the human host spatially and temporally. The "social proteome" is the subset of the environtome that influences the transition of proteomics technology to innovative applications in society. The social proteome encompasses, for example, new reimbursement schemes and business innovation models for proteomics diagnostics that depart from the "once-a-life-time" genotypic tests and the anticipated hype attendant to context and time sensitive proteomics tests. Building on the "nesting principle" for governance of complex systems as discussed by Elinor Ostrom, we propose here a 3-tiered organizational architecture for Big Data science such as

A half-life the divided life of Bruno Pontecorvo, physicist or spy

CERN Document Server

Close, Frank

2015-01-01

Bruno Pontecorvo dedicated his career to hunting for the Higgs boson of his day: the neutrino, a nearly massless particle considered essential to the process of nuclear fission. His work on the Manhattan project under Enrico Fermi confirmed his reputation as a brilliant physicist and helped usher in the nuclear age. He should have won a Nobel Prize, but late in the summer of 1950 he vanished. At the height of the Cold War, Pontecorvo had disappeared behind the Iron Curtain. In Half-Life, physicist and historian Frank Close offers a heretofore untold history of Pontecorvo’s life, based on unprecedented access to his friends, family, and colleagues. With all the elements of a Cold War thriller—classified atomic research, an infamous double agent, a kidnapping by Soviet operatives—Half-Life is a history of particle physics at perhaps its most powerful: when it created the bomb.

Molecular dynamics calculation of half-lives for thermal decay of Lennard-Jones clusters

International Nuclear Information System (INIS)

Smith, R.W.

1991-01-01

Molecular dynamics has been used with a Lenard-Jones (6-12) potential in order to study the decay behavior of neutral Argon clusters containing between 12 and 14 atoms. The clusters were heated to temperatures well above their melting points and then tracked in time via molecular dynamics until evaporation of one or more atoms was observed. In each simulation, the mode of evaporation, energy released during evaporation, and cluster lifetime were recorded. Results from roughly 2000 simulation histories were combined in order to compute statistically significant values of cluster half-lives and decay energies. It was found that cluster half-life decreases with increasing energy and that for a given value of excess energy (defined as E=(E tot -E gnd )/n), the 13 atom cluster is more stable against decay than clusters containing either 12 or 14 atoms. The dominant decay mechanism for all clusters was determined to be single atom emission. (orig.)

HALO--a Java framework for precise transcript half-life determination.

Science.gov (United States)

Friedel, Caroline C; Kaufmann, Stefanie; Dölken, Lars; Zimmer, Ralf

2010-05-01

Recent improvements in experimental technologies now allow measurements of de novo transcription and/or RNA decay at whole transcriptome level and determination of precise transcript half-lives. Such transcript half-lives provide important insights into the regulation of biological processes and the relative contributions of RNA decay and de novo transcription to differential gene expression. In this article, we present HALO (Half-life Organizer), the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription or decay determined with microarrays or RNA-seq. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command-line tools and a well-documented Java application programming interface (API). Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the provided user interfaces as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines. Source code, executables and documentation are available at http://www.bio.ifi.lmu.de/software/halo.

Variation in absorption and half-life of hydrocortisone influence plasma cortisol concentrations.

Science.gov (United States)

Hindmarsh, Peter C; Charmandari, Evangelia

2015-04-01

Hydrocortisone therapy should be individualized in congenital adrenal hyperplasia (CAH) patients to avoid over and under replacement. We have assessed how differences in absorption and half-life of cortisol influence glucocorticoid exposure. Forty-eight patients (21 M) aged between 6·1 and 20·3 years with CAH due to CYP21A2 deficiency were studied. Each patient underwent a 24-h plasma cortisol profile with the morning dose used to calculate absorption parameters along with an intravenous (IV) hydrocortisone (15 mg/m(2) body surface area) bolus assessment of half-life. Parameters derived were maximum plasma concentration (Cmax ), time of maximum plasma concentration (tmax ), time to attaining plasma cortisol concentration cortisol. Mean half-life was 76·5 ± 5·2 (range 40-225·3) min, Cmax 780·7 ± 61·6 nmol/l and tmax 66·7 (range 20-118) min. Time taken to a plasma cortisol concentration less than 100 nmol/l was 289 (range 140-540) min. Those with a fast half-life and slow tmax took longest to reach a plasma cortisol concentration less than 100 nmol/l (380 ± 34·6 min), compared to those with a slow half-life and fast tmax (298 ± 34·8 min) and those with a fast half-life and fast tmax (249·5 ± 14·4 min) (One-way anovaF = 4·52; P = 0·009). Both rate of absorption and half-life of cortisol in the circulation play important roles in determining overall exposure to oral glucocorticoid. Dose regimens need to incorporate estimates of these parameters into determining the optimum dosing schedule for individuals. © 2014 John Wiley & Sons Ltd.

Calculation of the biological half-life of radioactive isotopes

International Nuclear Information System (INIS)

Szabo, S.A.

1982-01-01

The biological half-life of 137 Cs and 90 Sr was determined based on K and Ca metabolism and on the considerable chemical similarity of K and Ca, carriers of Cs and Sr, resp. The tsub(1/2)=a/bxln2 formula was used for the calculation, where a is the quantity of the element in question, while b is the daily need of the animal for the given element. The biological half-life for cattle of both 137 Cs and 90 Sr was found to be 30 days, while that for swine 20 days and 35 days respectively. (Sz.J.)

Re-measurement of the half-life of sup 7 sup 9 Se

CERN Document Server

Jiang Song Sheng; Diao Li Jun; Li Chun Shen; GouJingRu; Wu Shao Yon

2002-01-01

A new attempt has been made for the re-measurement of the half-life of sup 7 sup 9 Se. We made two major improvements over our earlier sup 7 sup 9 Se half-life determination (Nucl. Instr. and Meth. B 123 (1997) 403). Firstly, the half-life of sup 7 sup 9 Se was measured relative to the precisely known half-life of sup 7 sup 5 Se, rather than an absolute measurement of sup 7 sup 9 Se/Se. Secondly, the Projectile X-ray Detection technique was used for the separation of sup 7 sup 9 Se from its isobar, sup 7 sup 9 Br, rather than measuring sup 8 sup 1 Br for the deduction of sup 7 sup 9 Br interference, and this technique was also used for separation of sup 7 sup 5 Se and its isobar, sup 7 sup 5 As. A detailed description of the sample preparations, experimental setup and measurements are given. The re-measured half-life of sup 7 sup 9 Se was (2.95+-0.38)x10 sup 5 a, about a factor of 3 lower than the previous value, 1.1x10 sup 6 a. The problems in the previous measurement are discussed.

The half-life of 207Bi and decays of 211At and 211Po

International Nuclear Information System (INIS)

Yanokura, M.; Kudo, H.; Nakahara, H.; Miyano, K.; Ohya, S.; Nitoh, O.

1978-01-01

The half-life of 207 Bi was obtained from the genetic relation between 207 Po and 207 Bi, and between 211 At and 207 Bi. The half-life was found to be 33.4 +- 0.8 y. The half-life of 207 Po was determined to be 5.81 +- 0.04 h by following the decay of the characteristic γ-rays from 207 Po. The half-life of 211 At was determined to be 7.23 +- 0.02 h by following the decay of γ-rays and α-particles from 211 At and 211 Po. The half-lives determined in the present work for 207 Po and 211 At agree with the literature although the half-life of 207 Bi differs considerably from the currently accepted value of 38 y. The branching ratio of 211 At decaying through EC and α-decay modes was determined together with the branching ratios of the three α-particles emitted from 211 Po. (Auth.)

Intrinsically Disordered Segments Affect Protein Half-Life in the Cell and during Evolution

Directory of Open Access Journals (Sweden)

Robin van der Lee

2014-09-01

Full Text Available Precise control of protein turnover is essential for cellular homeostasis. The ubiquitin-proteasome system is well established as a major regulator of protein degradation, but an understanding of how inherent structural features influence the lifetimes of proteins is lacking. We report that yeast, mouse, and human proteins with terminal or internal intrinsically disordered segments have significantly shorter half-lives than proteins without these features. The lengths of the disordered segments that affect protein half-life are compatible with the structure of the proteasome. Divergence in terminal and internal disordered segments in yeast proteins originating from gene duplication leads to significantly altered half-life. Many paralogs that are affected by such changes participate in signaling, where altered protein half-life will directly impact cellular processes and function. Thus, natural variation in the length and position of disordered segments may affect protein half-life and could serve as an underappreciated source of genetic variation with important phenotypic consequences.

Update of NIST half-life results corrected for ionization chamber source-holder instability

International Nuclear Information System (INIS)

Unterweger, M.P.; Fitzgerald, R.

2014-01-01

As reported at the ICRM 2011, it was discovered that the source holder used for calibrations in the NIST 4πγ ionization chamber (IC) was not stable. This has affected a large number of half-life measurement results previously reported and used in compilations of nuclear data. Corrections have been made on all of the half-life data based on the assumption that the changes to the ionization chamber response were gradual. The corrections are energy dependent and therefore radionuclide specific. This presentation will review our results and present the recommended changes in half-life values and/or uncertainties. - Highlights: • The NIST half-life data is corrected for sample positioning variations and refitted. • These results are reported and increased errors in the reported values are given. • Longer lived radionuclides are discussed

Validation of effective half-life of tritium and computation of dose at Madras Atomic Power Station

International Nuclear Information System (INIS)

Moolya, L.L.; Kannan, R.K.; Sreekumaran Nair, B.; Mohandas, P.G.; Rajan, R.

2001-01-01

In Pressurised Heavy Water Reactors (PHWRs) tritium is produced by the activation of deuterium present in the moderator and coolant system. Hence, the inventory of tritium in PHWR is high and it contributes about 20 percent of the Station Dose. Tritium enters body by inhalation, ingestion and skin absorption. Dose received by an individual depends on its elimination rate from the body and hence the effective half-life. It is found that the effective half-life varies from person to person. The effective half-life also depends on the weather condition. The variation of effective half-life is taken care of in dose estimation by average method. However, in case of dose calculation for single uptake cases, there is a need to take fixed effective half-life. ICRP has taken the effective half-life as 10 days. The effective half-life is taken as 6 days in Indian conditions based on the studies conducted earlier in MAPS and elsewhere. Now with available data for about 16 years a fresh study was conducted to validate the effective half-life. This paper gives the study of effective half-life of tritium and its variation during different seasons of the year in MAPS. This paper also gives methods used for computing dose due to tritium. (author)

Influence of sex and age on the biological half-life of cadmium in mice

International Nuclear Information System (INIS)

Taguchi, T.; Suzuki, S.

1981-01-01

The influence of age on the whole-body biological half-life of 109 Cd was studied in male mice following ip injection. The influence of sex on whole-body and organ retention was ascertained after sc injection. The whole-body biological half-life of 109 Cd of the older mice was more than twice that of the younger mice, and that of the female mice was longer than that of the males. These differences demonstrate a biological difference between males and females with respect to whole-body half-life of 109 Cd. The effects of age and sex on the biological half-life of Cd in mice are assessed quantitatively

Measurement of the 8Li half-life

International Nuclear Information System (INIS)

Flechard, X.; Lienard, E.; Naviliat-Cuncic, O.; Ban, G.; Carniol, B.; Etasse, D.; Fontbonne, J. M.; Rodriguez, D.; Lallena, A. M.; Alvarez, M. A. G.; Praena, J.

2010-01-01

We report a new measurement of the 8 Li half-life using a plastic scintillator and an ultrafast waveform digitizing module. The result, T 1/2 =(838.40±0.36) ms, improves by a factor of 2.5 the most precise result obtained so far and is furthermore deduced with negligible corrections due to dead time.

Half-life distribution table of radioactive nuclei

International Nuclear Information System (INIS)

Gugenberger, P.

1954-01-01

This table allows to identify an element if its period is known. Data for this table were taken from the half-life values adopted by Hollander, PERLMAN and SEABORG (Rev. mod. Phys., 1953, 22 number 2). Moreover for each nucleus, the mass number, the charge number and the type of decay are given in the table. (author) [fr

Potential fitness benefits of the half-pounder life history in Klamath River steelhead

Science.gov (United States)

Hodge, Brian W.; Wilzbach, Peggy; Duffy, Walter G.

2014-01-01

Steelhead Oncorhynchus mykiss from several of the world's rivers display the half-pounder life history, a variant characterized by an amphidromous (and, less often, anadromous) return to freshwater in the year of initial ocean entry. We evaluated factors related to expression of the half-pounder life history in wild steelhead from the lower Klamath River basin, California. We also evaluated fitness consequences of the half-pounder phenotype using a simple life history model that was parameterized with our empirical data and outputs from a regional survival equation. The incidence of the half-pounder life history differed among subbasins of origin and smolt ages. Precocious maturation occurred in approximately 8% of half-pounders and was best predicted by individual length in freshwater preceding ocean entry. Adult steelhead of the half-pounder phenotype were smaller and less fecund at age than adult steelhead of the alternative (ocean contingent) phenotype. However, our data suggest that fish of the half-pounder phenotype are more likely to spawn repeatedly than are fish of the ocean contingent phenotype. Models predicted that if lifetime survivorship were equal between phenotypes, the fitness of the half-pounder phenotype would be 17–28% lower than that of the ocean contingent phenotype. To meet the condition of equal fitness between phenotypes would require that first-year ocean survival be 21–40% higher among half-pounders in freshwater than among their cohorts at sea. We concluded that continued expression of the half-pounder phenotype is favored by precocious maturation and increased survival relative to that of the ocean contingent phenotype.

Relationship between isotope half-life and prostatic edema for optimal prostate dose coverage in permanent seed implants

International Nuclear Information System (INIS)

Villeneuve, Maxime; Leclerc, Ghyslain; Lessard, Etienne; Pouliot, Jean; Beaulieu, Luc

2008-01-01

The robustness of treatment planning to prostatic edema for three different isotopes ( 125 I, 103 Pd, and 131 Cs) is explored using dynamical dose calculations on 25 different clinical prostate cases. The treatment plans were made using the inverse planning by simulated annealing (IPSA) algorithm. The prescription was 144, 127, and 125 Gy for 125 I, 131 Cs, and 103 Pd, respectively. For each isotope, three dose distribution schemes were used to impose different protection levels to the urethra: V 120 =0%, V 150 =0%, and V 150 =30%. Eleven initial edema values were considered ranging from 1.0 (no edema) to 2.0 (100%). The edema was assumed to resolve exponentially with time. The prostate volume, seed positions, and seed activity were dynamically tracked to produce the final dose distribution. Edema decay half-lives of 10, 30, and 50 days were used. A total of 675 dynamical calculations were performed for each initial edema value. For the 125 I isotope, limiting the urethra V 120 to 0% leads to a prostate D 90 under 140 Gy for initial edema values above 1.5. Planning with urethra V 150 at 0% provides a good response to the edema; the prostate D 90 remains higher than 140 Gy for edema values up to 1.8 and a half-life of 30 days or less. For 103 Pd, the prostate D 90 is under 97% of the prescription dose for approximately 66%, 40%, and 30% of edema values for urethra V 120 =0%, V 150 =0%, and V 150 =30%, respectively. Similar behavior is seen for 131 Cs and the center of the prostate becomes 'cold' for almost all edema scenarios. The magnitude of the edema following prostate brachytherapy, as well as the half-life of the isotope used and that of the edema resorption, all have important impacts on the dose distribution. The 125 I isotope with its longer half-life is more robust to prostatic edema. Setting up good planning objectives can provide an adequate compromise between organ doses and robustness. This is even more important since seed misplacements will contribute

On the half-life of luminescence signals in dosimetric applications: A unified presentation

Science.gov (United States)

Pagonis, V.; Kitis, G.; Polymeris, G. S.

2018-06-01

Luminescence signals from natural and man-made materials are widely used in dosimetric and dating applications. In general, there are two types of half-lives of luminescence signals which are of importance to experimental and modeling work in this research area. The first type of half-life is the time required for the population of the trapped charge in a single trap to decay to half its initial value. The second type of half-life is the time required for the luminescence intensity to drop to half of its initial value. While there a handful of analytical expressions available in the literature for the first type of half-life, there are no corresponding analytical expressions for the second type. In this work new analytical expressions are derived for the half-life of luminescence signals during continuous wave optical stimulation luminescence (CW-OSL) or isothermal luminescence (ITL) experiments. The analytical expressions are derived for several commonly used luminescence models which are based on delocalized transitions involving the conduction band: first and second order kinetics, empirical general order kinetics (GOK), mixed order kinetics (MOK) and the one-trap one-recombination center (OTOR) model. In addition, half-life expressions are derived for a different type of luminescence model, which is based on localized transitions in a random distribution of charges. The new half-life expressions contain two parts. The first part is inversely proportional to the thermal or optical excitation rate, and depends on the experimental conditions and on the cross section of the relevant luminescence process. The second part is characteristic of the optical and/or thermal properties of the material, as expressed by the parameters in the model. A new simple and quick method for analyzing luminescence signals is developed, and examples are given of applying the new method to a variety of dosimetric materials. The new test allows quick determination of whether a set of

Building ProteomeTools based on a complete synthetic human proteome

Science.gov (United States)

Zolg, Daniel P.; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J.; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

2018-01-01

The ProteomeTools project builds molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we report the generation and multimodal LC-MS/MS analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products and exemplify the utility of this data. The resource will be extended to >1 million peptides and all data will be shared with the community via ProteomicsDB and proteomeXchange. PMID:28135259

Radioactive source simulation for half-life experiment

International Nuclear Information System (INIS)

Wanitsuksombut, Warapon; Decthyothin, Chanti

1999-01-01

A simulation of radioactivity decay by using programmable light source with a few minutes half-life is suggested. A photodiode with digital meter label in cps is use instead of radiation detector. Both light source and photodiode are installed in a black box to avoid surrounding room light. The simulation set can also demonstrate Inverse Square Law experiment of radiation penetration. (author)

The half-life of 125I

International Nuclear Information System (INIS)

Simpson, B.R.S.; Meyer, B.R.

1989-01-01

The Bureau International des Poids et Mesures (BIPM) organized an international comparison of activity measurements of a solution of 125 I. The half-life value adopted was 59.5±0.4d. The large uncertainty took account of a recently published value (Schrader, 1986) which is considerably lower than the widely used value of 60.0±0.1d. The present work, which was undertaken at the suggestion of the BIPM, has yielded a value which confirms the lower measurement. (author)

Incubation and Growth of Life Sciences, Medical and Biotechnology Businesses in Proteomics, Genomics, Medicine, and Dentistry

Science.gov (United States)

2007-04-01

Medical and Biotechnology Businesses in Proteomics , Genomics, Medicine, and Dentistry PRINCIPAL INVESTIGATOR: Mark S. Long Brian C...2007 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Incubation and Growth of Life Sciences, Medical and Biotechnology Businesses in Proteomics ...aflatoxins B1 and G1 from Aspergillus flavus. All toxins studied were purchased from Sigma Aldrich and used without further purification. Solutions

Determination of disintegration half-life of 252Cf

International Nuclear Information System (INIS)

Chen Keliang; Liu Guoxing; Wang Sufang; Zheng Jiwen

1991-01-01

The follow-up measurements have been made by using a Si(Au) detector with small solid angle geometry for α disintegration of 252 Cf. The measured half-life of disintegration is 2.638 ± 0.009 year. This value is in accordance with other previous results

Biogeoscience from a Metallomic and Proteomic Perspective

Science.gov (United States)

Anbar, A. D.; Shock, E.

2004-12-01

In the wake of the genomics revolution, life scientists are expanding their focus from the genome to the "proteome" - the assemblage of all proteins in a cell - and the "metallome" - the distribution of inorganic species in a cell. The proteome and metallome are tightly connected because proteins and protein products are intimately involved in the transport and homeostasis of inorganic elements, and because many enzymes depend on inorganic elements for catalytic activity. Together, they are at the heart of metabolic function. Unlike the relatively static genome, the proteome and metallome are extremely dynamic, changing rapidly in response to environmental cues. They are substantially more complex than the genome; for example, in humans, some 30,000 genes code for approximately 500,000 proteins. Metaphorically, the proteome and metallome constitute the complex, dynamic "language" by which the genome and the environment communicate. Therefore biogeochemists, like life scientists, are moving beyond a strictly genomic perspective. Research guided by proteomic and metallomic perspectives and methodologies should provide new insights into the connections between life and the inorganic Earth in modern environments, and the evolution of these connections through time. For example, biogeochemical research in modern environments, such as Yellowstone hot springs, is hindered by the gap between genomic determinations of metabolic potential in ecosystems and geochemical characterizations of the energetic boundary conditions faced by these ecosystems; genomics tells us "who is there" and geochemistry tells us "what they might be doing", but neither genomics nor geochemistry easily provide quantitative information about which metabolisms are actually active or a framework for understanding why ecosystems do not fully exploit the energy available in their surroundings. Such questions are fundamentally kinetic rather than thermodynamic and therefore demand that we characterize and

Extending the half-life of a fab fragment through generation of a humanized anti-human serum albumin Fv domain: An investigation into the correlation between affinity and serum half-life.

Science.gov (United States)

Adams, Ralph; Griffin, Laura; Compson, Joanne E; Jairaj, Mark; Baker, Terry; Ceska, Tom; West, Shauna; Zaccheo, Oliver; Davé, Emma; Lawson, Alastair Dg; Humphreys, David P; Heywood, Sam

2016-10-01

We generated an anti-albumin antibody, CA645, to link its Fv domain to an antigen-binding fragment (Fab), thereby extending the serum half-life of the Fab. CA645 was demonstrated to bind human, cynomolgus, and mouse serum albumin with similar affinity (1-7 nM), and to bind human serum albumin (HSA) when it is in complex with common known ligands. Importantly for half-life extension, CA645 binds HSA with similar affinity within the physiologically relevant range of pH 5.0 - pH 7.4, and does not have a deleterious effect on the binding of HSA to neonatal Fc receptor (FcRn). A crystal structure of humanized CA645 Fab in complex with HSA was solved and showed that CA645 Fab binds to domain II of HSA. Superimposition with the crystal structure of FcRn bound to HSA confirmed that CA645 does not block HSA binding to FcRn. In mice, the serum half-life of humanized CA645 Fab is 84.2 h. This is a significant extension in comparison with Fab variant. The Fab-HSA structure was used to design a series of mutants with reduced affinity to investigate the correlation between the affinity for albumin and serum half-life. Reduction in the affinity for MSA by 144-fold from 2.2 nM to 316 nM had no effect on serum half-life. Strikingly, despite a reduction in affinity to 62 µM, an extension in serum half-life of 26.4 h was still obtained. CA645 Fab and the CA645 Fab-HSA complex have been deposited in the Protein Data Bank (PDB) with accession codes, 5FUZ and 5FUO, respectively.

Nonoscillation of half-linear dynamic equations

Czech Academy of Sciences Publication Activity Database

Matucci, S.; Řehák, Pavel

2010-01-01

Roč. 60, č. 5 (2010), s. 1421-1429 ISSN 0898-1221 R&D Projects: GA AV ČR KJB100190701 Grant - others:GA ČR(CZ) GA201/07/0145 Institutional research plan: CEZ:AV0Z10190503 Keywords : half-linear dynamic equation * time scale * (non)oscillation * Riccati technique Subject RIV: BA - General Mathematics Impact factor: 1.472, year: 2010 http://www.sciencedirect.com/science/article/pii/S0898122110004384

Update of NIST half-life results corrected for ionization chamber source-holder instability.

Science.gov (United States)

Unterweger, M P; Fitzgerald, R

2014-05-01

As reported at the ICRM 2011, it was discovered that the source holder used for calibrations in the NIST 4πγ ionization chamber (IC) was not stable. This has affected a large number of half-life measurement results previously reported and used in compilations of nuclear data. Corrections have been made on all of the half-life data based on the assumption that the changes to the ionization chamber response were gradual. The corrections are energy dependent and therefore radionuclide specific. This presentation will review our results and present the recommended changes in half-life values and/or uncertainties. © 2013 Published by Elsevier Ltd.

Neutron activation analyses and half-life measurements at the usgs triga reactor

Science.gov (United States)

Larson, Robert E.

Neutron activation of materials followed by gamma spectroscopy using high-purity germanium detectors is an effective method for making measurements of nuclear beta decay half-lives and for detecting trace amounts of elements present in materials. This research explores applications of neutron activation analysis (NAA) in two parts. Part 1. High Precision Methods for Measuring Decay Half-Lives, Chapters 1 through 8 Part one develops research methods and data analysis techniques for making high precision measurements of nuclear beta decay half-lives. The change in the electron capture half-life of 51Cr in pure chromium versus chromium mixed in a gold lattice structure is explored, and the 97Ru electron capture decay half-life are compared for ruthenium in a pure crystal versus ruthenium in a rutile oxide state, RuO2. In addition, the beta-minus decay half-life of 71mZn is measured and compared with new high precision findings. Density Functional Theory is used to explain the measured magnitude of changes in electron capture half-life from changes in the surrounding lattice electron configuration. Part 2. Debris Collection Nuclear Diagnostic at the National Ignition Facility, Chapters 9 through 11 Part two explores the design and development of a solid debris collector for use as a diagnostic tool at the National Ignition Facility (NIF). NAA measurements are performed on NIF post-shot debris collected on witness plates in the NIF chamber. In this application NAA is used to detect and quantify the amount of trace amounts of gold from the hohlraum and germanium from the pellet present in the debris collected after a NIF shot. The design of a solid debris collector based on material x-ray ablation properties is given, and calculations are done to predict performance and results for the collection and measurements of trace amounts of gold and germanium from dissociated hohlraum debris.

The impact of extended half-life versus conventional factor product on hemophilia caregiver burden.

Science.gov (United States)

Schwartz, Carolyn E; Powell, Victoria E; Su, Jun; Zhang, Jie; Eldar-Lissai, Adi

2018-05-01

Extended half-life factor products have reduced annualized bleeding rates in hemophilia patients. The impact of extended half-life versus conventional factor products on hemophilia caregiver burden has not been investigated. This study aimed to evaluate caregiver burden in extended half-life versus conventional factor products for hemophilia A and B. This cross-sectional web-based study of caregivers of people with hemophilia A or B was recruited from a panel research company and by word of mouth. Participants completed the Hemophilia Caregiver Impact measure, the PedsQL Family Impact Module (PedsQL), and the Work Productivity and Activity Impairment Questionnaire (WPAI). We also collected demographic, insurance coverage, and medical information related to the hemophilia patient(s). Burden differences were assessed using linear regression and matched cohort analyses. The sample (n = 448) included 49 people who were caring for people on extended half-life factor products. Worse caregiver burden was associated with more infusions per week and more bleeds in the past 6 months. Regression analyses suggested that caring for someone who is on a extended half-life factor product is associated with lower emotional impact (β = - 0.11, p factor product had lower Emotional Impact and Practical Impact scores (t = - 2.95 and - 2.94, respectively, p factor product infusions of extended half-life factor products appears to reduce the emotional distress and practical burden of caregiving. Future work should evaluate the longitudinal impact.

Superior serum half life of albumin tagged TNF ligands

International Nuclear Information System (INIS)

Mueller, Nicole; Schneider, Britta; Pfizenmaier, Klaus; Wajant, Harald

2010-01-01

Due to their immune stimulating and apoptosis inducing properties, ligands of the TNF family attract increasing interest as therapeutic proteins. A general limitation of in vivo applications of recombinant soluble TNF ligands is their notoriously rapid clearance from circulation. To improve the serum half life of the TNF family members TNF, TWEAK and TRAIL, we genetically fused soluble variants of these molecules to human serum albumin (HSA). The serum albumin-TNF ligand fusion proteins were found to be of similar bioactivity as the corresponding HSA-less counterparts. Upon intravenous injection (i.v.), serum half life of HSA-TNF ligand fusion proteins, as determined by ELISA, was around 15 h as compared to approximately 1 h for all of the recombinant control TNF ligands without HSA domain. Moreover, serum samples collected 6 or 24 h after i.v. injection still contained high TNF ligand bioactivity, demonstrating that there is only limited degradation/inactivation of circulating HSA-TNF ligand fusion proteins in vivo. In a xenotransplantation model, significantly less of the HSA-TRAIL fusion protein compared to the respective control TRAIL protein was required to achieve inhibition of tumor growth indicating that the increased half life of HSA-TNF ligand fusion proteins translates into better therapeutic action in vivo. In conclusion, our data suggest that genetic fusion to serum albumin is a powerful and generally applicable mean to improve bioavailability and in vivo activity of TNF ligands.

On the biological half-life of caesium in pregnant women and infants

International Nuclear Information System (INIS)

Rundo, J.; Turner, F.M.

1992-01-01

In the 1960s, changes were observed in the levels of 137 Cs in women who were pregnant or who had recently given birth. These were not associated with changes in the rate of fall-out, and were interpreted as the consequences of changes in the biological half-life. It was deduced that the biological half-life of caesium just before parturition averaged 59% of the value (87±33 days) after the birth of the baby; and that there was a step change at parturition. The behaviour of the levels during pregnancy suggested there was a gradual decrease in the biological half-life. Similar measurements were made in very young children. The concentration of the radionuclide in a breast-fed baby was usually a little less than that in the mother, indicating some discrimination in the transfer from plasma to milk; the concentration in a bottle-fed baby increased substantially and rapidly from the level at or shortly after birth. Data for three babies were sufficiently extensive to permit determination of the biological half-life in each. Values of 8.7±0.6 days, 15.4±1.1 days, and 14.9±3.6 days were derived. (author)

Improving the control of systematic uncertainties in precision measurements of radionuclide half-life

International Nuclear Information System (INIS)

Towers, S.

2013-01-01

Many experiments designed to precisely determine the half-life of a radionuclide employ a long lived reference source to help determine the impact on the data of any systematic variation in the detector and associated electronics. The half-life of the radionuclide of interest is determined from the ratio of its decay rate data to the decay rate data from the reference source. This correction procedure assumes that any underlying systematic affects the data and reference measurements in exactly the same way. In this paper we show that when some systematic effects affect the two differently, the ratio procedure can leave artifacts in the corrected data that can compromise an unbiased and precise assessment of the radionuclide half-life. We describe two methods that can help overcome this problem. We also describe several statistical tests that help determine which effects may underlie systematic variations in the data. We discuss an illustrative example based on previously published 32 Si and 36 Cl data recorded by an experiment at Brookhaven National Laboratory. We correct the data for systematic variation related to climate variation and estimate the 32 Si half-life to be T 1/2 =171.8±1.8. The reduction in uncertainty in the 32 Si half-life, relative to the previous estimate based upon this data, is equivalent to that which would be achieved through increasing the size of the data set by almost 3.5 times. - Author-Highlights: • Isotope decay data and reference source data can have differing systematics. • Differing systematics can inflate uncertainty of isotope half-life estimate. • We describe two methods to overcome this problem. • We describe statistical tests to determine which variables cause systematics. • We analyze Brookhaven 32Si/36Cl decay data as an illustrative example

High-precision half-life determination for 21Na using a 4 π gas-proportional counter

Science.gov (United States)

Finlay, P.; Laffoley, A. T.; Ball, G. C.; Bender, P. C.; Dunlop, M. R.; Dunlop, R.; Hackman, G.; Leslie, J. R.; MacLean, A. D.; Miller, D.; Moukaddam, M.; Olaizola, B.; Severijns, N.; Smith, J. K.; Southall, D.; Svensson, C. E.

2017-08-01

A high-precision half-life measurement for the superallowed β+ transition between the isospin T =1 /2 mirror nuclei 21Na and 21Ne has been performed at the TRIUMF-ISAC radioactive ion beam facility yielding T1 /2=22.4506 (33 ) s, a result that is a factor of 4 more precise than the previous world-average half-life for 21Na and represents the single most precisely determined half-life for a transition between mirror nuclei to date. The contribution to the uncertainty in the 21Na F tmirror value due to the half-life is now reduced to the level of the nuclear-structure-dependent theoretical corrections, leaving the branching ratio as the dominant experimental uncertainty.

Half-life and intensities of photons of 103Pd isotope

International Nuclear Information System (INIS)

Popov, Yu.S.; Zakharova, L.V.; Kupriyanov, V.N.; Andreev, O.I.; Pakhomov, A.N.; Vakhetov, F.Z.

2001-01-01

Half-life and intensities of photons forming during 103 Pd isotope decay are determined by the methods of semiconductor x-ray and γ-spectrometry. 103 Pd is applied in nuclear medicine for preparation of 103m Rh isomer (T 1/2 =56 min) being used in irradiation of prostate neoplasms. Half-life of 103 Pd isotope is 16±0.6 days, relative intensities of x-ray and γ-photons are: K α /Kβ=5.1±0.4; 358 keV - 100 rel.units; 295 keV - 12.3±0.4 rel.units; 497 keV - 17.6±0.6 rel.units. Errors are represented for confidence probability 95 % [ru

Half-life data--a critical review of TECDOC-619 update

International Nuclear Information System (INIS)

Woods, M.J.; Collins, S.M.

2004-01-01

An accurate knowledge of selected nuclear decay data is critical to a wide range of processes involving radionuclides. An IAEA publication in 1991 was dedicated to the evaluation of half-lives and specific gamma-ray emission probabilities for 39 selected radionuclides considered to be important for detector efficiency calibrations. A new exercise was initiated in December 1998 to update this previous evaluation and to include a number of new radionuclides of interest; 62 radionuclides were considered along with specific parent-daughter combinations (to give a total of 64 radionuclides). That work is now being completed and a new set of recommended data is being prepared for publication. A critical comparison of the 1991 and 2003 half-life data suggests that there has not been any significant improvement in the accuracy of the recommended data. The possible reasons for this situation are discussed together with the evaluation procedure and the quality of the available data. Proposals are made for concerted actions that could lead to a significant improvement in these recommended half-life data

Effect of change in half-life of Se-79 on the safety of HLW geological disposal system

International Nuclear Information System (INIS)

Ishihara, Yoshinao; Ishiguro, Katsuhiko; Umeki, Hiroyuki

1999-11-01

Se-79 is one of key radionuclides in the performance assessment of the geological disposal system. Based on recent measurements, it is possible that the half-life of Se-79 will be changed longer than the present value in most handbooks and tables of isotopes. This study presents performance assessment calculations to investigate the overall effect of change in half-life of Se-79 on the repository system safety. The total system performance analyses for Se-79 were carried out, which focussed on the Reference-Case of the safety assessment in the H12 Project. As results, the maximum release rate in Becquerel unit of Se-79 from the engineered barrier system with new half-life decreases about one order of magnitude than that with half-life used so far. It is, however, that the maximum release rate in Becquerel unit of Se-79 from the natural barrier system is almost same for both half-life because of the channelling effects of groundwater flow. Consequently, the calculated maximum dose rate of Se-79 with new half-life does not change. It can be concluded that the change in half-life of Se-79 does not affect overall safety of the H12 disposal concept. (author)

Standardization of 40 K by liquid scintillation counting. Determination of the half-life

International Nuclear Information System (INIS)

Grau Carles, A.; Grau Malonda, A.

1997-01-01

The relative abundance of the natural radioisotope ''40 K in environmental samples frequently generates interferences in low activity measurements. In the present study we propose the determination of ''40 K by the CIEMAT/NIST method. On this context, the verification of ''40 K half-life is required. We present a half-life value obtained by liquid scintillation counting in excellent agreement with those reported in the literature. (Author)

Tests of a Fast Plastic Scintillator for High-Precision Half-Life Measurements

Science.gov (United States)

Laffoley, A. T.; Dunlop, R.; Finlay, P.; Leach, K. G.; Michetti-Wilson, J.; Rand, E. T.; Svensson, C. E.; Grinyer, G. F.; Thomas, J. C.; Ball, G.; Garnsworthy, A. B.; Hackman, G.; Orce, J. N.; Triambak, S.; Williams, S. J.; Andreoiu, C.; Cross, D.

2013-03-01

A fast plastic scintillator detector is evaluated for possible use in an ongoing program of high-precision half-life measurements of short lived β emitters. Using data taken at TRI-UMF's Isotope Separator and Accelerator Facility with a radioactive 26Na beam, a detailed investigation of potential systematic effects with this new detector setup is being performed. The technique will then be applied to other β-decay half-life measurements including the superallowed Fermi β emitters 10C, 14O, and T = 1/2 decay of 15O.

Near-optimum procedure for half-life measurement by high-resolution gamma-ray spectrometry

International Nuclear Information System (INIS)

Parker, J.L.

1989-01-01

A near-optimum procedure for using high-resolution γ-ray spectrometry to measure the half-lives of appropriate γ-ray- emitting-nuclides is presented. Among the important points of the procedure are the employment of the reference source method for implicit correction of pileup and deadtime losses; the use of full-energy peak-area ratios as the fundamental measured quantities; and continuous, high-rate data acquisition to obtain good results in a fraction of a half-life if desired. Equations are given for estimating the precision of the computed half-lives in terms of total measurement time, number of spectral acquisitions, and the precision of peak-area ratios. Results of 169 Yb half-life measurements are given as an example of the procedure's application. 3 refs., 2 tabs

Precision half-life measurement of 11C: The most precise mirror transition F t value

Science.gov (United States)

Valverde, A. A.; Brodeur, M.; Ahn, T.; Allen, J.; Bardayan, D. W.; Becchetti, F. D.; Blankstein, D.; Brown, G.; Burdette, D. P.; Frentz, B.; Gilardy, G.; Hall, M. R.; King, S.; Kolata, J. J.; Long, J.; Macon, K. T.; Nelson, A.; O'Malley, P. D.; Skulski, M.; Strauss, S. Y.; Vande Kolk, B.

2018-03-01

Background: The precise determination of the F t value in T =1 /2 mixed mirror decays is an important avenue for testing the standard model of the electroweak interaction through the determination of Vu d in nuclear β decays. 11C is an interesting case, as its low mass and small QE C value make it particularly sensitive to violations of the conserved vector current hypothesis. The present dominant source of uncertainty in the 11CF t value is the half-life. Purpose: A high-precision measurement of the 11C half-life was performed, and a new world average half-life was calculated. Method: 11C was created by transfer reactions and separated using the TwinSol facility at the Nuclear Science Laboratory at the University of Notre Dame. It was then implanted into a tantalum foil, and β counting was used to determine the half-life. Results: The new half-life, t1 /2=1220.27 (26 ) s, is consistent with the previous values but significantly more precise. A new world average was calculated, t1/2 world=1220.41 (32 ) s, and a new estimate for the Gamow-Teller to Fermi mixing ratio ρ is presented along with standard model correlation parameters. Conclusions: The new 11C world average half-life allows the calculation of a F tmirror value that is now the most precise value for all superallowed mixed mirror transitions. This gives a strong impetus for an experimental determination of ρ , to allow for the determination of Vu d from this decay.

Proteomics in Argentina - limitations and future perspectives: A special emphasis on meat proteomics.

Science.gov (United States)

Fadda, Silvina; Almeida, André M

2015-11-01

Argentina is one of the most relevant countries in Latin America, playing a major role in regional economics, culture and science. Over the last 80 years, Argentinean history has been characterized by several upward and downward phases that had major consequences on the development of science in the country and most recently on proteomics. In this article, we characterize the evolution of Proteomics sciences in Argentina over the last decade and a half. We describe the proteomics publication output of the country in the framework of the regional and international contexts, demonstrating that Argentina is solidly anchored in a regional context, showing results similar to other emergent and Latin American countries, albeit still far from the European, American or Australian realities. We also provide a case-study on the importance of Proteomics to a specific sector in the area of food science: the use of bacteria of technological interest, highlighting major achievements obtained by Argentinean proteomics scientists. Finally, we provide a general picture of the endeavors being undertaken by Argentinean Proteomics scientists and their international collaborators to promote the Proteomics-based research with the new generation of scientists and PhD students in both Argentina and other countries in the Southern cone. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative analysis of proteome and lipidome dynamics reveals functional regulation of global lipid metabolism

DEFF Research Database (Denmark)

Casanovas, Albert; Sprenger, Richard R; Tarasov, Kirill

2015-01-01

Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular...

Pre-Clinical Intravenous Serum Pharmacokinetics of Albumin Binding and Non-Half-Life Extended Nanobodies®

Directory of Open Access Journals (Sweden)

Sven Hoefman

2015-07-01

Full Text Available Nanobodies are antigen-binding, single variable domain proteins derived from naturally-occurring, heavy chain only antibodies. They are highly soluble, stable, and can be linked to build multi-specific formats. Several Nanobodies are currently in clinical development in different therapeutic areas, for both chronic and acute applications. For the former, prolonged exposure is achieved by half-life extending moieties that target endogenous albumin, while for the latter, non-half-life extended constructs are preferable. To demonstrate the general pharmacokinetic behavior of both formats, serum levels of seven intravenously administered Nanobodies were analyzed in cynomolgus monkeys, mice or rabbits. In monkeys, the total clearance of a monomeric irrelevant Nanobody was rapid (2.0 mL/(min*kg and approximated the species glomerular filtration rate, indirectly suggesting that the Nanobody was mainly eliminated via the kidneys. When linked to an anti-albumin Nanobody, a 376-fold decrease in clearance was observed, resulting in a terminal half-life of 4.9 days, corresponding to the expected species albumin half-life. Similar conclusions were drawn for (non- half-life extended mono-, bi- and trimeric Nanobodies in mice or rabbits, suggesting that these kinetic principles apply across species. Applying this knowledge to species translation and study design is crucial for successful pre-clinical development of novel therapeutic Nanobody candidates.

Half-life of each dioxin and PCB congener in the human body

Energy Technology Data Exchange (ETDEWEB)

Ogura, Isamura [National Institute of Advanced Industrial Science and Technology, Tsukuba (Japan)

2004-09-15

It is well known that dioxin and PCB congeners accumulate in the human body. For assessing their toxicological risk, it is important to know the half-life of each congener in the human body. This study summarizes the overall half-lives of congeners in humans as reported in the literature, and compares them with the half-lives due to fecal and sebum excretions, as estimated by data on the concentrations of congeners in feces and sebum in the literature. In addition, the overall half-lives of congeners for the general Japanese population were estimated from the data on dietary intakes and concentrations in the human body reported by the municipalities.

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

DEFF Research Database (Denmark)

Welker, F.

2018-01-01

Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identificati......Background: The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein...... not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against......), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations...

Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome.

Science.gov (United States)

Lange, Philipp F; Huesgen, Pitter F; Nguyen, Karen; Overall, Christopher M

2014-04-04

A goal of the Chromosome-centric Human Proteome Project is to identify all human protein species. With 3844 proteins annotated as "missing", this is challenging. Moreover, proteolytic processing generates new protein species with characteristic neo-N termini that are frequently accompanied by altered half-lives, function, interactions, and location. Enucleated and largely void of internal membranes and organelles, erythrocytes are simple yet proteomically challenging cells due to the high hemoglobin content and wide dynamic range of protein concentrations that impedes protein identification. Using the N-terminomics procedure TAILS, we identified 1369 human erythrocyte natural and neo-N-termini and 1234 proteins. Multiple semitryptic N-terminal peptides exhibited improved mass spectrometric identification properties versus the intact tryptic peptide enabling identification of 281 novel erythrocyte proteins and six missing proteins identified for the first time in the human proteome. With an improved bioinformatics workflow, we developed a new classification system and the Terminus Cluster Score. Thereby we described a new stabilizing N-end rule for processed protein termini, which discriminates novel protein species from degradation remnants, and identified protein domain hot spots susceptible to cleavage. Strikingly, 68% of the N-termini were within genome-encoded protein sequences, revealing alternative translation initiation sites, pervasive endoproteolytic processing, and stabilization of protein fragments in vivo. The mass spectrometry proteomics data have been deposited to ProteomeXchange with the data set identifier .

An albumin-oligonucleotide assembly for potential combinatorial drug delivery and half-life extension applications

DEFF Research Database (Denmark)

Kuhlmann, Matthias; Hamming, Jonas Bohn Refslund; Voldum, Anders

2017-01-01

The long blood circulatory property of human serum albumin, due to engagement with the cellular recycling neonatal Fc receptor (FcRn), is an attractive drug half-life extension enabling technology. This work describes a novel site-specific albumin double-stranded (ds) DNA assembly approach, in wh...... technology platform that offers potential combinatorial drug delivery and half-life extension applications.......The long blood circulatory property of human serum albumin, due to engagement with the cellular recycling neonatal Fc receptor (FcRn), is an attractive drug half-life extension enabling technology. This work describes a novel site-specific albumin double-stranded (ds) DNA assembly approach......, in which the 3' or 5' end maleimide-derivatized oligodeoxynucleotides are conjugated to albumin cysteine at position 34 (cys34) and annealed with complementary strands to allow single site-specific protein modification with functionalized ds oligodeoxynucleotides. Electrophoretic gel shift assays...

Designing of peptides with desired half-life in intestine-like environment

KAUST Repository

Sharma, Arun; Singla, Deepak; Rashid, Mamoon; Raghava, Gajendra Pal Singh

2014-01-01

hindered mainly because of their high susceptibility towards proteases degradation. We have developed an in silico method to predict the half-life of peptides in intestine-like environment and to design better peptides having optimized physicochemical

[Methods of quantitative proteomics].

Science.gov (United States)

Kopylov, A T; Zgoda, V G

2007-01-01

In modern science proteomic analysis is inseparable from other fields of systemic biology. Possessing huge resources quantitative proteomics operates colossal information on molecular mechanisms of life. Advances in proteomics help researchers to solve complex problems of cell signaling, posttranslational modification, structure and functional homology of proteins, molecular diagnostics etc. More than 40 various methods have been developed in proteomics for quantitative analysis of proteins. Although each method is unique and has certain advantages and disadvantages all these use various isotope labels (tags). In this review we will consider the most popular and effective methods employing both chemical modifications of proteins and also metabolic and enzymatic methods of isotope labeling.

ESOL facility for the generation and radiochemical separation of short half-life fission products

International Nuclear Information System (INIS)

Gehrke, R.J.; Meikrantz, D.H.; Baker, J.D.; Anderl, R.A.; Novick, V.J.; Greenwood, R.C.

1988-01-01

A facility has been developed at the Idaho National Engineering Laboratory (INEL) for the generation and rapid radiochemical separation of short half-life mixed fission products. This facility, referred to as the Idaho Elemental Separation On Line (ESOL), consists of electro-plated sources of spontaneously fissioning 252 Cf with a helium jet transport arrangement to continuously deliver short half-life, mixed fission products to the radiochemistry laboratory for rapid, computer controlled, radiochemical separations. 18 refs., 13 figs

A formula for half-life of proton radioactivity

Science.gov (United States)

Zhang, Zhi-Xing; Dong, Jian-Min

2018-01-01

We present a formula for proton radioactivity half-lives of spherical proton emitters with the inclusion of the spectroscopic factor. The coefficients in the formula are calibrated with the available experimental data. As an input to calculate the half-life, the spectroscopic factor that characterizes the important information on nuclear structure should be obtained with a nuclear many-body approach. This formula is found to work quite well, and in better agreement with experimental measurements than other theoretical models. Therefore, it can be used as a powerful tool in the investigation of proton emission, in particular for experimentalists. Supported by National Natural Science Foundation of China (11435014, 11405223, 11675265, 11575112), the 973 Program of China (2013CB834401, 2013CB834405), National Key Program for S&T Research and Development (2016YFA0400501), the Knowledge Innovation Project (KJCX2-EW-N01) of Chinese Academy of Sciences, the Funds for Creative Research Groups of China (11321064) and the Youth Innovation Promotion Association of Chinese Academy of Sciences

Spontaneous formation and dynamics of half-skyrmions in a chiral liquid-crystal film

Science.gov (United States)

Nych, Andriy; Fukuda, Jun-Ichi; Ognysta, Uliana; Žumer, Slobodan; Muševič, Igor

2017-12-01

Skyrmions are coreless vortex-like excitations emerging in diverse condensed-matter systems, and real-time observation of their dynamics is still challenging. Here we report the first direct optical observation of the spontaneous formation of half-skyrmions. In a thin film of a chiral liquid crystal, depending on experimental conditions including film thickness, they form a hexagonal lattice whose lattice constant is a few hundred nanometres, or appear as isolated entities with topological defects compensating their charge. These half-skyrmions exhibit intriguing dynamical behaviour driven by thermal fluctuations. Numerical calculations of real-space images successfully corroborate the experimental observations despite the challenge because of the characteristic scale of the structures close to the optical resolution limit. A thin film of a chiral liquid crystal thus offers an intriguing platform that facilitates a direct investigation of the dynamics of topological excitations such as half-skyrmions and their manipulation with optical techniques.

Precision half-life measurement of .sup.140 La with Ge-detector

Czech Academy of Sciences Publication Activity Database

Adam, Jindřich; Belov, A. G.; Brandt, R.; Chaloun, P.; Honusek, Milan; Kalinnikov, V. G.; Krivopustov, M. I.; Kulakov, B. A.; Langrock, E. J.; Pronskikh, V. S.; Sosnin, A. N.; Stegailov, V. I.; Tsoupko-Sitnikov, V. M.; Wan, J. S.; Westmeier, W.

2002-01-01

Roč. 187, - (2002), s. 419-426 ISSN 0168-583X R&D Projects: GA AV ČR KSK1048102 Keywords : radioastive nuclei * Ge-detectors * half-life measurements Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.158, year: 2002

Molecular system analysis, multidimensional, dynamic, ultra-sensitive exploration of proteomes

International Nuclear Information System (INIS)

Scharattenholz, A.; Soski, V.; Stegmann, W.; Schroer, K.; Godovac-Zimmermann, J.; Cabuk, A.; Pejovi, V.; Wozny, W.; Cahill, M.A.; Drukier, A.K.; Volkovitsky, P.

2001-01-01

ProteoSys AG's holistic proteomics strategy extends beyond classical proteome research as a new paradigm. Our concept of multidimensional molecular systems analysis of complex model systems employs the innovative ProteoDyn TM approach. This enables us to correlate dynamic changes of proteomes with their biophysical and biochemical environment. Our supersensitive Multi Photon Detection (MPD) technology enables ultra-sensitive detection of proteins, deep into the low abundance domain. Our technology platform includes the affinity analysis of phospho- and glyco-proteomes, and with our 'fish hook' methods we can capture and fully characterize even serpentine G-coupled receptors and associated proteins, including routine comprehensive post-translational analyses performed by a well equipped mass spectrometry group. Throughput and quality is obtained by automation and high end robotics, with data management handled by a dedicated bioinformatics department. Thus ProteoSys AG has a range of state of the art and proprietary tools at its disposal to analyse even the most difficult complex model systems. MPD is an isotopic detection method proprietary to ProteoSys For MPD analysis we have implemented protocols where over 99% of proteins can be iodinated, and where the iodinated proteins can be identified by mass spectrometry. Because MPD measures the energy of detected particles, it can discriminate between signals originating from different isotopes co-electrophoresed by 2D-PAGE. Thus MPD imagers have a 'multicolour' functionality suitable for differential display and improved throughput, eliminating inter-gel variations. Importantly, MPD opens up not only the world of detection of low abundance proteins, but also identification and characterization. Radioactive low abundance protein spots containing less than one attomole of protein can be excised from a 2D-gel, mixed with unlabelled proteins, and 'tracked' by MPD. The identity of the labeled protein is determined by

Characterization of ubiquitination dependent dynamics in growth factor receptor signaling by quantitative proteomics

DEFF Research Database (Denmark)

Akimov, Vyacheslav; Rigbolt, Kristoffer T G; Nielsen, Mogens M

2011-01-01

Protein ubiquitination is a dynamic reversible post-translational modification that plays a key role in the regulation of numerous cellular processes including signal transduction, endocytosis, cell cycle control, DNA repair and gene transcription. The conjugation of the small protein ubiquitin...... investigating ubiquitination on a proteomic scale, mainly due to the inherited complexity and heterogeneity of ubiquitination. We describe here a quantitative proteomics strategy based on the specificity of ubiquitin binding domains (UBDs) and Stable Isotope Labeling by Amino acids in Cell culture (SILAC...... as ubiquitination-dependent events in signaling pathways. In addition to a detailed seven time-point profile of EGFR ubiquitination over 30 minutes of ligand stimulation, our data determined prominent involvement of Lysine-63 ubiquitin branching in EGF signaling. Furthermore, we found two centrosomal proteins, PCM1...

High-Precision Half-Life Measurement for the Superallowed β+ Emitter Alm26

Science.gov (United States)

Finlay, P.; Ettenauer, S.; Ball, G. C.; Leslie, J. R.; Svensson, C. E.; Andreoiu, C.; Austin, R. A. E.; Bandyopadhyay, D.; Cross, D. S.; Demand, G.; Djongolov, M.; Garrett, P. E.; Green, K. L.; Grinyer, G. F.; Hackman, G.; Leach, K. G.; Pearson, C. J.; Phillips, A. A.; Sumithrarachchi, C. S.; Triambak, S.; Williams, S. J.

2011-01-01

A high-precision half-life measurement for the superallowed β+ emitter Alm26 was performed at the TRIUMF-ISAC radioactive ion beam facility yielding T1/2=6346.54±0.46stat±0.60systms, consistent with, but 2.5 times more precise than, the previous world average. The Alm26 half-life and ft value, 3037.53(61) s, are now the most precisely determined for any superallowed β decay. Combined with recent theoretical corrections for isospin-symmetry-breaking and radiative effects, the corrected Ft value for Alm26, 3073.0(12) s, sets a new benchmark for the high-precision superallowed Fermi β-decay studies used to test the conserved vector current hypothesis and determine the Vud element of the Cabibbo-Kobayashi-Maskawa quark mixing matrix.

Proteomic analysis of the Theileria annulata schizont

Science.gov (United States)

Witschi, M.; Xia, D.; Sanderson, S.; Baumgartner, M.; Wastling, J.M.; Dobbelaere, D.A.E.

2013-01-01

The apicomplexan parasite, Theileria annulata, is the causative agent of tropical theileriosis, a devastating lymphoproliferative disease of cattle. The schizont stage transforms bovine leukocytes and provides an intriguing model to study host/pathogen interactions. The genome of T. annulata has been sequenced and transcriptomic data are rapidly accumulating. In contrast, little is known about the proteome of the schizont, the pathogenic, transforming life cycle stage of the parasite. Using one-dimensional (1-D) gel LC-MS/MS, a proteomic analysis of purified T. annulata schizonts was carried out. In whole parasite lysates, 645 proteins were identified. Proteins with transmembrane domains (TMDs) were under-represented and no proteins with more than four TMDs could be detected. To tackle this problem, Triton X-114 treatment was applied, which facilitates the extraction of membrane proteins, followed by 1-D gel LC-MS/MS. This resulted in the identification of an additional 153 proteins. Half of those had one or more TMD and 30 proteins with more than four TMDs were identified. This demonstrates that Triton X-114 treatment can provide a valuable additional tool for the identification of new membrane proteins in proteomic studies. With two exceptions, all proteins involved in glycolysis and the citric acid cycle were identified. For at least 29% of identified proteins, the corresponding transcripts were not present in the existing expressed sequence tag databases. The proteomics data were integrated into the publicly accessible database resource at EuPathDB (www.eupathdb.org) so that mass spectrometry-based protein expression evidence for T. annulata can be queried alongside transcriptional and other genomics data available for these parasites. PMID:23178997

Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components

DEFF Research Database (Denmark)

Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Po

2014-01-01

To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during...... replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors...... such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment...

The Use of Gene Ontology Term and KEGG Pathway Enrichment for Analysis of Drug Half-Life.

Directory of Open Access Journals (Sweden)

Yu-Hang Zhang

Full Text Available A drug's biological half-life is defined as the time required for the human body to metabolize or eliminate 50% of the initial drug dosage. Correctly measuring the half-life of a given drug is helpful for the safe and accurate usage of the drug. In this study, we investigated which gene ontology (GO terms and biological pathways were highly related to the determination of drug half-life. The investigated drugs, with known half-lives, were analyzed based on their enrichment scores for associated GO terms and KEGG pathways. These scores indicate which GO terms or KEGG pathways the drug targets. The feature selection method, minimum redundancy maximum relevance, was used to analyze these GO terms and KEGG pathways and to identify important GO terms and pathways, such as sodium-independent organic anion transmembrane transporter activity (GO:0015347, monoamine transmembrane transporter activity (GO:0008504, negative regulation of synaptic transmission (GO:0050805, neuroactive ligand-receptor interaction (hsa04080, serotonergic synapse (hsa04726, and linoleic acid metabolism (hsa00591, among others. This analysis confirmed our results and may show evidence for a new method in studying drug half-lives and building effective computational methods for the prediction of drug half-lives.

Redox proteomics and the dynamic molecular landscape of the aging brain.

Science.gov (United States)

Perluigi, Marzia; Swomley, Aaron M; Butterfield, D Allan

2014-01-01

It is well established that the risk to develop neurodegenerative disorders increases with chronological aging. Accumulating studies contributed to characterize the age-dependent changes either at gene and protein expression level which, taken together, show that aging of the human brain results from the combination of the normal decline of multiple biological functions with environmental factors that contribute to defining disease risk of late-life brain disorders. Finding the "way out" of the labyrinth of such complex molecular interactions may help to fill the gap between "normal" brain aging and development of age-dependent diseases. To this purpose, proteomics studies are a powerful tool to better understand where to set the boundary line of healthy aging and age-related disease by analyzing the variation of protein expression levels and the major post translational modifications that determine "protein" physio/pathological fate. Increasing attention has been focused on oxidative modifications due to the crucial role of oxidative stress in aging, in addition to the fact that this type of modification is irreversible and may alter protein function. Redox proteomics studies contributed to decipher the complexity of brain aging by identifying the proteins that were increasingly oxidized and eventually dysfunctional as a function of age. The purpose of this review is to summarize the most important findings obtained by applying proteomics approaches to murine models of aging with also a brief overview of some human studies, in particular those related to dementia. Copyright © 2014. Published by Elsevier B.V.

Ubiquitin-fusion as a strategy to modulate protein half-life: A3G antiviral activity revisited

International Nuclear Information System (INIS)

Cadima-Couto, Iris; Freitas-Vieira, Acilino; Nowarski, Roni; Britan-Rosich, Elena; Kotler, Moshe; Goncalves, Joao

2009-01-01

The human APOBEC3G (A3G) is a potent inhibitor of HIV-1 replication and its activity is suppressed by HIV-1 virion infectivity factor (Vif). Vif neutralizes A3G mainly by inducing its degradation in the proteasome and blocking its incorporation into HIV-1 virions. Assessing the time needed for A3G incorporation into virions is, therefore, important to determine how quickly Vif must act to induce its degradation. We show that modelling the intracellular half-life of A3G can induce its Vif-independent targeting to the ubiquitin-proteasome system. By using various amino acids (X) in a cleavable ubiquitin-X-A3G fusion, we demonstrate that the half-life (t1/2) of X-A3G can be manipulated. We show that A3G molecules with a half-life of 13 min are incorporated into virions, whereas those with a half-life shorter than 5 min were not. The amount of X-A3G incorporated into virions increases from 13 min (Phe-A3G) to 85 min (Asn-A3G) and remains constant after this time period. Interestingly, despite the presence of similar levels of Arg-A3G (t1/2 = 28 min) and Asp-A3G (t1/2 = 65 min) into HIV-1 Δvif virions, inhibition of viral infectivity was only evident in the presence of A3G proteins with a longer half-life (t1/2 ≥ 65 min).

Application of genetic algorithms for determination biological half-life of 137 Cs in milk

International Nuclear Information System (INIS)

Pantelic, G.

1998-01-01

Genetic algorithm an optimization method involving natural selection mechanisms, was used to determine biological half-life of sup 1 sup 3 sup 7 Cs in the milk, after the Chernobyl accident, based on a two compartment linear system model. Genetic algorithms operate on populations of strings. Reproduction, crossover and mutation are applied to successive string population to create new string population. A model parameter estimation is performed by minimizing square differences between fitting function and experimental data. The calculated biological half-life of sup 1 sup 3 sup 7 Cs in milk is (32(+(-) days (author)

A novel strategy for global analysis of the dynamic thiol redox proteome.

Science.gov (United States)

Martínez-Acedo, Pablo; Núñez, Estefanía; Gómez, Francisco J Sánchez; Moreno, Margoth; Ramos, Elena; Izquierdo-Álvarez, Alicia; Miró-Casas, Elisabet; Mesa, Raquel; Rodriguez, Patricia; Martínez-Ruiz, Antonio; Dorado, David Garcia; Lamas, Santiago; Vázquez, Jesús

2012-09-01

Nitroxidative stress in cells occurs mainly through the action of reactive nitrogen and oxygen species (RNOS) on protein thiol groups. Reactive nitrogen and oxygen species-mediated protein modifications are associated with pathophysiological states, but can also convey physiological signals. Identification of Cys residues that are modified by oxidative stimuli still poses technical challenges and these changes have never been statistically analyzed from a proteome-wide perspective. Here we show that GELSILOX, a method that combines a robust proteomics protocol with a new computational approach that analyzes variance at the peptide level, allows a simultaneous analysis of dynamic alterations in the redox state of Cys sites and of protein abundance. GELSILOX permits the characterization of the major endothelial redox targets of hydrogen peroxide in endothelial cells and reveals that hypoxia induces a significant increase in the status of oxidized thiols. GELSILOX also detected thiols that are redox-modified by ischemia-reperfusion in heart mitochondria and demonstrated that these alterations are abolished in ischemia-preconditioned animals.

High-precision half-life measurements of the T =1 /2 mirror β decays 17F and 33Cl

Science.gov (United States)

Grinyer, J.; Grinyer, G. F.; Babo, M.; Bouzomita, H.; Chauveau, P.; Delahaye, P.; Dubois, M.; Frigot, R.; Jardin, P.; Leboucher, C.; Maunoury, L.; Seiffert, C.; Thomas, J. C.; Traykov, E.

2015-10-01

Background: Measurements of the f t values for T =1 /2 mirror β+ decays offer a method to test the conserved vector current hypothesis and to determine Vud, the up-down matrix element of the Cabibbo-Kobayashi-Maskawa matrix. In most mirror decays used for these tests, uncertainties in the f t values are dominated by the uncertainties in the half-lives. Purpose: Two precision half-life measurements were performed for the T =1 /2 β+ emitters, 17F and 33Cl, in order to eliminate the half-life as the leading source of uncertainty in their f t values. Method: Half-lives of 17F and 33Cl were determined using β counting of implanted radioactive ion beam samples on a moving tape transport system at the Système de Production d'Ions Radioactifs Accélérés en Ligne low-energy identification station at the Grand Accélérateur National d'Ions Lourds. Results: The 17F half-life result, 64.347 (35) s, precise to ±0.05 % , is a factor of 5 times more precise than the previous world average. The half-life of 33Cl was determined to be 2.5038 (22) s. The current precision of ±0.09 % is nearly 2 times more precise compared to the previous world average. Conclusions: The precision achieved during the present measurements implies that the half-life no longer dominates the uncertainty of the f t values for both T =1 /2 mirror decays 17F and 33Cl.

$\\beta$-decay half-life of $^{70}$Kr a bridge nuclide for the rp-process beyond A = 70

CERN Document Server

Oinonen, M; Jokinen, A; Baumann, P; Didierjean, François; Huck, A; Knipper, A; Ramdhane, M; Walter, G; Van Duppen, P; Huyse, M; Marguier, G; Novikov, Yu N; Popov, A; Seliverstov, D M; Schatz, H

2000-01-01

The $\\beta$-decay half-life of $^{70}$Kr has been measured for the first time at the ISOLDE PSB Facility at CERN. Mass separated $^{70}$Kr ions were produced by 1 GeV proton induced spallation reactions in a Nb foil. The measured half-life is 57(21) ms. This value is consistent with the half-life calculated assuming a pure Fermi decay, but is clearly lower than the value used in a recent rp-process reaction flow calculation. The result shows that the reaction flow via two-proton-capture of $^{68}$Se is 2.5 times faster than previously calculated assuming an astrophysical temperature of 1.5 GK and a density of 10$^{6}$g/cm$^{3}$.

Dynamic heterogeneity in life histories

DEFF Research Database (Denmark)

Tuljapurkar, Shripad; Steiner, Uli; Orzack, Steven Hecht

2009-01-01

or no fixed heterogeneity influences this trait. We propose that dynamic heterogeneity provides a 'neutral' model for assessing the possible role of unobserved 'quality' differences between individuals. We discuss fitness for dynamic life histories, and the implications of dynamic heterogeneity...... generate dynamic heterogeneity: life-history differences produced by stochastic stratum dynamics. We characterize dynamic heterogeneity in a range of species across taxa by properties of the Markov chain: the entropy, which describes the extent of heterogeneity, and the subdominant eigenvalue, which...... distributions of lifetime reproductive success. Dynamic heterogeneity contrasts with fixed heterogeneity: unobserved differences that generate variation between life histories. We show by an example that observed distributions of lifetime reproductive success are often consistent with the claim that little...

Calculation of chemical elimination half-life from blood with an ongoing exposure source: the example of perfluorooctanoic acid (PFOA).

Science.gov (United States)

Russell, Mark H; Waterland, Robert L; Wong, Fiona

2015-06-01

Determination of the chemical clearance rate from human blood is a critical component of toxicokinetic exposure assessment. Analysis of temporal biomonitoring data without consideration of ongoing exposure results in calculation of apparent elimination half-life values that are longer than the intrinsic value. The intrinsic elimination half-life is solely a function of the rate of elimination while the apparent elimination half-life reflects the processes of both elimination and ongoing exposure. Confusion between intrinsic and apparent half-life values can lead to misinterpretation of biomonitoring data and can result in exaggerated predictions in subsequent modeling efforts. This work provides a review of the first-order equations that have been developed to calculate intrinsic and apparent half-life values and the potential bias that can result from confusing these two values. Published human biomonitoring data for perfluorooctanoic acid (PFOA) are analyzed using these equations to provide examples of low, medium and high bias in determination of the intrinsic elimination half-life from plasma or serum, the components of blood typically analyzed for PFOA. An approach is also provided to estimate the extent of exposure reduction that is indicated by declining longitudinal or cross-sectional biomonitoring data. Based on the evaluation methodology presented in this work, the intrinsic elimination half-life of PFOA in humans is 2.4years, representing the average of independent estimates of 2.5years (95% CI, 2.4-2.7) and 2.3years (95% CI, 2.1-2.4). The declining concentration of PFOA in blood of the general USA adult population represents an estimated exposure reduction of 20-30% over the period 1999-2008. Copyright © 2014 Elsevier Ltd. All rights reserved.

Farm animal proteomics - A review

DEFF Research Database (Denmark)

Bendixen, Emøke; Danielsen, Marianne; Hollung, Kristin

2011-01-01

In agricultural sciences as in all other areas of life science, the implementation of proteomics and other post-genomic tools is an important step towards more detailed understanding of the complex biological systems that control physiology and pathology of living beings. Farm animals are raised...... and cattle are relevant not only for farm animal sciences, but also for adding to our understanding of complex biological mechanisms of health and disease in humans. The aim of this review is to present an overview of the specific topics of interest within farm animal proteomics, and to highlight some...... of the areas where synergy between classic model organism proteomics and farm animal proteomics is rapidly emerging. Focus will be on introducing the special biological traits that play an important role in food production, and on how proteomics may help optimize farm animal production...

High-Precision Half-life Measurements for the Superallowed β+ Emitter 14O

Science.gov (United States)

Laffoley, A. T.; Svensson, C. E.; Andreoiu, C.; Austin, R. A. E.; Ball, G. C.; Blank, B.; Bouzomita, H.; Cross, D. S.; Diaz Varela, A.; Dunlop, R.; Finlay, P.; Garnsworthy, A. B.; Garrett, P. E.; Giovinazzo, J.; Grinyer, G. F.; Hackman, G.; Hadinia, B.; Jamieson, D. S.; Ketelhut, S.; Leach, K. G.; Leslie, J. R.; Tardiff, E. R.; Thomas, J. C.; Unsworth, C.

2014-03-01

The half-life of 14O, a superallowed Fermi β+ emitter, has been determined via simultaneous γ and β counting experiments at TRIUMF's Isotope Separator and Accelerator facility. Following the implantation of 14O samples at the center of the 8π spectrometer, a γ counting measurement was performed by detecting the 2313 keV γ-rays emitted from the first excited state of the daughter 14N using 20 high-purity germanium (HPGe) detectors. A simultaneous β counting experiment was performed using a fast plastic scintillator positioned directly behind the implantation site. The results, T½(γ) = 70:632 ± 0:094 s and T½(β) = 70:610 ± 0:030 s, are consistent with one another and, together with eight previous measurements, establish a new average for the 14O half-life of T½ = 70:619 ± 0:011 s with a reduced χ2 of 0.99.

A New Method to Determine the Half-Life for Penicillin Using Microcalorimeter

Science.gov (United States)

Li, Z. X.; Zhao, W. W.

2015-01-01

The dissolution process of penicillin in normal saline and isotonic glucose solution was reported using a microcalorimeter. Both the integral and differential heats of solution were measured. The quantitative relationships between the amount of heat released and the quantity of dissolved penicillin were established. Meanwhile, the kinetics and the half-life of the dissolution processes as well as the enthalpy of solution, the entropy of dissolution, and the free energy of dissolution were determined. The results showed that a change of the solvent from normal saline to isotonic glucose solution had little effect on the half-life of penicillin in the dissolution process, and there was no significant difference between the stabilities of penicillin in isotonic glucose solution and normal saline. Moreover, the dissolution process of penicillin in isotonic glucose solution followed the first-order kinetics. These results could provide a theoretical basis for the clinical applications of penicillin.

Determination of {sup 126}Sn half-life from ICP-MS and gamma spectrometry measurements

Energy Technology Data Exchange (ETDEWEB)

Bienvenu, P.; Arnal, N.; Comte, J. [CEA Cadarache DEN/DEC/SA3C/LARC, Paul Lez Durance (France); Ferreux, L.; Lepy, M.C.; Be, M.M. [CEA Saclay LIST LNE/LNHB, Gif sur Yvette (France); Andreoletti, G. [AREVA Cogema SL/UP2-800, Beaumont Hague (France)

2009-07-01

A new value of {sup 126}Sn half-life was determined by combination of inductively coupled plasma-mass spectrometry (ICP-MS) and gamma spectrometry measurements on purified sample solutions collected from nuclear fuel reprocessing. {sup 126}Sn was isolated through dissolution of fission product precipitates and liquid-liquid extraction with N-benzoyl-N-phenyl-hydroxylamine (BPHA). The abundance of {sup 126}Sn atoms together with the absence of interfering species in the analysed solutions made it possible to measure both mass concentration and nuclide activity with high precision and accuracy. This led to a {sup 126}Sn half-life value of 1.980 (57) x 10{sup 5} a. (orig.)

Increased Functional Half-life of Fibroblast Growth Factor-1 by Recovering a Vestigial Disulfide Bond

Directory of Open Access Journals (Sweden)

Jihun Lee

2010-12-01

Full Text Available The fibroblast growth factor (FGF family of proteins contains an absolutely conserved Cys residue at position 83 that is present as a buried free cysteine. We have previously shown that mutation of the structurally adjacent residue, Ala66, to cysteine results in the formation of a stabilizing disulfide bond in FGF-1. This result suggests that the conserved free cysteine residue at position 83 in the FGF family of proteins represents a vestigial half-cystine. Here, we characterize the functional half-life and mitogenic activity of the oxidized form of the Ala66Cys mutation to identify the effect of the recovered vestigial disulfide bond between Cys83 and Cys66 upon the cellular function of FGF-1. The results show that the mitogenic activity of this mutant is significantly increased and that its functional half-life is greatly extended. These favorable effects are conferred by the formation of a disulfide bond that simultaneously increases thermodynamic stability of the protein and removes a reactive buried thiol at position 83. Recovering this vestigial disulfide by introducing a cysteine at position 66 is a potentially useful protein engineering strategy to improve the functional half-life of other FGF family members.

Measurements of Actual Effective Half - Life in 131I Therapy for Graves' Hyperthyroidism

International Nuclear Information System (INIS)

So, Yong Seon; Kim, Myung Seon; Kwon, Ki Hyun; Kim, Seok Whan; Kim, Tae Hyung; Han, Sang Woong; Kim, Eun Sil; Kim, Chong Soon

1996-01-01

Radioiodine[131I] has been used for the treatment of Graves' hyperthyroidism since the late 1940's and is now generally regarded as the treatment of choice for Graves' hyperthyroidism who does not remit following a course of antithyroid drugs. But for the dose given, several different protocols have been described by different centers, each attempting to reduce the incidence of long-term hypothyroidism while maintaining an acceptable rate control of Graves' hyperthyroidism. Our goals were to evaluate effective half-life and predict absorbed dose in Graves' hyperthyroidism patients, therefore, to calculate and read minister radioiodine activity needed to achieve aimed radiation dose. Our data showed that the mean effective 131I half-life for Graves' disease is 5.3 days(S.D=0.88) and mean biologic half-life is 21 days, range 9.5-67.2 days. The mean administered activity and the mean values of absorbed doses wet: 532 MBq(S.D.=254), 112 Gy (S.D.=50.9), respectively. The mean activity needed to achieve aimed radiation dose were 51 MBq and marked differences of 131I thyroidal uptake between tracer and therapy occurred in our study. We are sure that the dose calculation method that uses 5 days thyroidal 131I uptake measurements after tracer and therapy dose, provides sufficient data about the effective treatment in Graves' hyperthyroidism.

Half Life - The divided life of Bruno Maximovitch Pontecorvo

CERN Multimedia

CERN. Geneva

2016-01-01

When Bruno Pontecorvo fled to the USSR at the height of the Cold War in 1950, half way through his life, the British Government, MI5 and FBI tried to portray him as scientifically insignificant, and to imply that his disappearance posed no threat to the West. In reality Pontecorvo was already one of the leading experts in nuclear physics, and recently declassified papers reveal that a prime agenda of FBI and MI5 was to cover up their errors. . During his time in the USSR he made major contributions to physics, and justified the sobriquet: "Mr Neutrino". This talk will reveal the background to his sudden flight, and also evaluate his work in theoretical physics in the aftermath of his arrival in Dubna. Previously secret documents now show that he proposed the concept of associated production before Gell Mann and Pais, and he had an idea to discover the neutrino at a reactor. He may be considered the father of neutrino astronomy with his successful prediction that neutrinos from a supernova could be detected, b...

The Redox Proteome*

Science.gov (United States)

Go, Young-Mi; Jones, Dean P.

2013-01-01

The redox proteome consists of reversible and irreversible covalent modifications that link redox metabolism to biologic structure and function. These modifications, especially of Cys, function at the molecular level in protein folding and maturation, catalytic activity, signaling, and macromolecular interactions and at the macroscopic level in control of secretion and cell shape. Interaction of the redox proteome with redox-active chemicals is central to macromolecular structure, regulation, and signaling during the life cycle and has a central role in the tolerance and adaptability to diet and environmental challenges. PMID:23861437

High-precision half-life and branching-ratio measurements for superallowed Fermi β+ emitters at TRIUMF - ISAC

Science.gov (United States)

Laffoley, A. T.; Dunlop, R.; Finlay, P.; Grinyer, G. F.; Andreoiu, C.; Austin, R. A. E.; Ball, G. C.; Bandyopadhyay, D.; Blank, B.; Bouzomita, H.; Chagnon-Lessard, S.; Chester, A.; Cross, D. S.; Demand, G.; Diaz Varela, A.; Djongolov, M.; Ettenauer, S.; Garnsworthy, A. B.; Garrett, P. E.; Giovinazzo, J.; Glister, J.; Green, K. L.; Hackman, G.; Hadinia, B.; Jamieson, D. S.; Ketelhut, S.; Leach, K. G.; Leslie, J. R.; Pearson, C. J.; Phillips, A. A.; Rand, E. T.; Starosta, K.; Sumithrarachchi, C. S.; Svensson, C. E.; Tardiff, E. R.; Thomas, J. C.; Towner, I. S.; Triambak, S.; Unsworth, C.; Williams, S. J.; Wong, J.; Yates, S. W.; Zganjar, E. F.

2014-03-01

A program of high-precision half-life and branching-ratio measurements for superallowed Fermi β emitters is being carried out at TRIUMF's Isotope Separator and Accelerator (ISAC) radioactive ion beam facility. Recent half-life measurements for the superallowed decays of 14O, 18Ne, and 26Alm, as well as branching-ratio measurements for 26Alm and 74Rb are reported. These results provide demanding tests of the Standard Model and the theoretical isospin symmetry breaking (ISB) corrections in superallowed Fermi β decays.

Determination of half life of tellurium isotopes: a proposal for the teaching of nuclear physics

International Nuclear Information System (INIS)

Ruivo, Julio C.; Zamboni, Cibele B.; Batista, Wagner F.

2013-01-01

This work aimed at the development of courseware for teaching nuclear physics, using experimental data of half-life measurement (T1/2) of Tellurium isotopes (A=127 and 131). The choice of Tellurium was established for providing nuclear data, which are fundamental in related investigations of nuclear structure and its use in various areas such as geochemistry, chemical and pharmaceutical industries, astrophysics etc. For evaluation of the proposal performance, the material was made available, bringing a lot of information about nuclear safety, production and storage of radioactive material and concepts of radioactive decay, subatomic particles, emission of gamma radiation, half-life, etc.

Determination of half life of tellurium isotopes: a proposal for the teaching of nuclear physics

Energy Technology Data Exchange (ETDEWEB)

Ruivo, Julio C.; Zamboni, Cibele B.; Batista, Wagner F., E-mail: julio.ruivo.costa@usp.br, E-mail: czamboni@ipen.br, E-mail: fisicawagner@gmail.com [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2013-07-01

This work aimed at the development of courseware for teaching nuclear physics, using experimental data of half-life measurement (T1/2) of Tellurium isotopes (A=127 and 131). The choice of Tellurium was established for providing nuclear data, which are fundamental in related investigations of nuclear structure and its use in various areas such as geochemistry, chemical and pharmaceutical industries, astrophysics etc. For evaluation of the proposal performance, the material was made available, bringing a lot of information about nuclear safety, production and storage of radioactive material and concepts of radioactive decay, subatomic particles, emission of gamma radiation, half-life, etc.

Study of the half-life of 123I and the determination of possible radionuclidic impurities

International Nuclear Information System (INIS)

Delgado, Jose Ubiratan; Araujo, Miriam Taina Ferreira de; Silva, Carlos Jose da; Araujo, Camila Cristina Cunha; Candido, Marcos Antonio; Pereira, Wagner do Prado

2013-01-01

During the process of production of the radiopharmaceutical nuclear reactor or cyclotron, impurities can be generated from biological, chemical and radionuclidic. The development of the present work was to study the half-life of Na 123 I sample produced in IEN (Institute of Nuclear Engineering) using the technique of gamma-ray spectrometry with germanium detector in order to Identify such impurities. The results Indicate values of half-life consistent with recent publications with a deviation of 0,08% and 0:11% of uncertainty as well as the identification of impurities to radionuclides 95m Tc, 96 Tc and 121 Te. (author)

The HP 9825 A program for the determination of an isotope half-life

International Nuclear Information System (INIS)

Jujuratisbela, Uju.

1980-01-01

Determination of half life of gold 198, indium 116, manganese 56, copper 64 are presented, using least squares method in HP 9825 A. This method is more accurate and needs less time than graphic method. (author tr.)

Proteomic responses reveal the differential effects induced by cadmium in mussels Mytilus galloprovincialis at early life stages.

Science.gov (United States)

Xu, Lanlan; Peng, Xiao; Yu, Deliang; Ji, Chenglong; Zhao, Jianmin; Wu, Huifeng

2016-08-01

Cadmium (Cd) has become an important metal contaminant and posed severe risk on the organisms in the coastal environments of the Bohai Sea. Marine mussel Mytilus galloprovincialis is widely distributed along the Bohai coast and consumed as seafood by local residents. Evidences indicate that the early stages of marine organisms are more sensitive to metal contaminants. In this study, we applied two-dimensional electrophoresis-based proteomics to characterize the biological effects of Cd (50 μg L(-1)) in the early life stages (D-shape larval and juvenile) of mussels. The different proteomic responses demonstrated the differential responsive mechanisms to Cd exposure in these two early life stages of mussels. In details, results indicated that Cd mainly induced immune and oxidative stresses in both D-shape larval and juvenile mussels via different pathways. In addition, the significant up-regulation of triosephosphate isomerase and metallothionein confirmed the enhanced energy demand and mobilized detoxification mechanism in D-shape larval mussels exposed to Cd. In juvenile mussels, Cd exposure also induced clear apoptosis. Overall, this work suggests that Cd is a potential immune toxicant to mussel M. galloprovincialis at early life stages. Copyright © 2016 Elsevier Ltd. All rights reserved.

Work Dissatisfaction and Sleep Problems among Canadians in the Latter Half of Life.

Science.gov (United States)

Brown, Kyla; Bierman, Alex

2017-09-01

This study examined the relationship between work dissatisfaction and sleep problems among Canadian adults in the latter half of life, as well as how gender and social contact moderate this relationship. Data were obtained from the Canadian General Social Survey, Cycle 21 (2007), which sampled adults aged 45 and older in 2007. Analyses focused on individuals with employment as their main activity. Analyses show that work dissatisfaction positively predicts trouble sleeping. There are no significant gender differences in this relationship. Social contact with friends buffers this relationship, but social contact with family does not, and buffering does not vary significantly between men and women. This research contributes to knowledge on sleep problems by showing that work dissatisfaction is adversely associated with sleep problems among Canadians in the latter half of life, but social contact with friends can weaken this deleterious relationship.

Xylem sap proteomics.

Science.gov (United States)

de Bernonville, Thomas Dugé; Albenne, Cécile; Arlat, Matthieu; Hoffmann, Laurent; Lauber, Emmanuelle; Jamet, Elisabeth

2014-01-01

Proteomic analysis of xylem sap has recently become a major field of interest to understand several biological questions related to plant development and responses to environmental clues. The xylem sap appears as a dynamic fluid undergoing changes in its proteome upon abiotic and biotic stresses. Unlike cell compartments which are amenable to purification in sufficient amount prior to proteomic analysis, the xylem sap has to be collected in particular conditions to avoid contamination by intracellular proteins and to obtain enough material. A model plant like Arabidopsis thaliana is not suitable for such an analysis because efficient harvesting of xylem sap is difficult. The analysis of the xylem sap proteome also requires specific procedures to concentrate proteins and to focus on proteins predicted to be secreted. Indeed, xylem sap proteins appear to be synthesized and secreted in the root stele or to originate from dying differentiated xylem cells. This chapter describes protocols to collect xylem sap from Brassica species and to prepare total and N-glycoprotein extracts for identification of proteins by mass spectrometry analyses and bioinformatics.

New evaluation of alpha decay half-life of 190Pt isotope for the Pt-Os dating system

International Nuclear Information System (INIS)

Tavares, O.A.P.; Medeiros, E.L.; Terranova, M.L.

2005-08-01

A semiempirical model based on the quantum mechanical tunnelling mechanism of alpha emission from nuclei has been used to evaluate the half-life of the Pt isotopes. For the important naturally occurring 190 Pt isotope, the radiogenic parent in the 190 Pt → 186 Os dating system, the model yielded a half-life value of (3.7± 0.3) versus 10 11 y. This is comparable to (3.2±0.1) versus 10 11 y which was obtained in the last direct counting experiment to measure the alpha activity of 190 Pt (Tavares and Terranova, Rad. Measurem. 27 (1997) 19). A literature survey of available alpha decay half-life values for 190 Pt isotope is also reported. The significant discrepancies found between data obtained by direct counting, indirect geological methods and different calculation models are analysed and discussed. (author)

High-precision half-life measurements of the T=1/2 mirror beta decays F-17 and Cl-33

OpenAIRE

Grinyer, J; Grinyer, G. F; Babo, Mathieu; Bouzomita, H; Chauveau, P; Delahaye, P; Dubois, M; Frigot, R; Jardin, P; Leboucher, C; Maunoury, L; Seiffert, C; Thomas, J. C; Traykov, E

2015-01-01

Background: Measurements of the ft values for T=1/2 mirror β+ decays offer a method to test the conserved vector current hypothesis and to determine Vud, the up-down matrix element of the Cabibbo-Kobayashi-Maskawa matrix. In most mirror decays used for these tests, uncertainties in the ft values are dominated by the uncertainties in the half-lives. Purpose: Two precision half-life measurements were performed for the T=1/2β+ emitters, 17F and 33Cl, in order to eliminate the half-life as th...

High-precision half-life measurements of the T=1/2 mirror β decays F17 and Cl33

OpenAIRE

Grinyer, J; Grinyer, G F; Babo, M; Bouzomita, H; Chauveau, P; Delahaye, P; Dubois, M; Frigot, R; Jardin, P; Leboucher, C; Maunoury, L; Seiffert, C; Thomas, J C; Traykov, E

2015-01-01

Background: Measurements of the ft values for T=1/2 mirror β+ decays offer a method to test the conserved vector current hypothesis and to determine Vud, the up-down matrix element of the Cabibbo-Kobayashi-Maskawa matrix. In most mirror decays used for these tests, uncertainties in the ft values are dominated by the uncertainties in the half-lives. Purpose: Two precision half-life measurements were performed for the T=1/2β+ emitters, F17 and Cl33, in order to eliminate the half-life as the le...

Peculiarities in power type comparison results for half-linear dynamic equations

Czech Academy of Sciences Publication Activity Database

Řehák, Pavel

2012-01-01

Roč. 42, č. 6 (2012), s. 1995-2013 ISSN 0035-7596 R&D Projects: GA AV ČR KJB100190701 Institutional support: RVO:67985840 Keywords : half-linear dynamic equation * time scale * comparison theorem Subject RIV: BA - General Mathematics Impact factor: 0.389, year: 2012 http://projecteuclid.org/euclid.rmjm/1361800616

Quantitative proteomics and dynamic imaging of the nucleolus reveal distinct responses to UV and ionizing radiation.

Science.gov (United States)

Moore, Henna M; Bai, Baoyan; Boisvert, François-Michel; Latonen, Leena; Rantanen, Ville; Simpson, Jeremy C; Pepperkok, Rainer; Lamond, Angus I; Laiho, Marikki

2011-10-01

The nucleolus is a nuclear organelle that coordinates rRNA transcription and ribosome subunit biogenesis. Recent proteomic analyses have shown that the nucleolus contains proteins involved in cell cycle control, DNA processing and DNA damage response and repair, in addition to the many proteins connected with ribosome subunit production. Here we study the dynamics of nucleolar protein responses in cells exposed to stress and DNA damage caused by ionizing and ultraviolet (UV) radiation in diploid human fibroblasts. We show using a combination of imaging and quantitative proteomics methods that nucleolar substructure and the nucleolar proteome undergo selective reorganization in response to UV damage. The proteomic responses to UV include alterations of functional protein complexes such as the SSU processome and exosome, and paraspeckle proteins, involving both decreases and increases in steady state protein ratios, respectively. Several nonhomologous end-joining proteins (NHEJ), such as Ku70/80, display similar fast responses to UV. In contrast, nucleolar proteomic responses to IR are both temporally and spatially distinct from those caused by UV, and more limited in terms of magnitude. With the exception of the NHEJ and paraspeckle proteins, where IR induces rapid and transient changes within 15 min of the damage, IR does not alter the ratios of most other functional nucleolar protein complexes. The rapid transient decrease of NHEJ proteins in the nucleolus indicates that it may reflect a response to DNA damage. Our results underline that the nucleolus is a specific stress response organelle that responds to different damage and stress agents in a unique, damage-specific manner.

Effect of parent and daughter deformation on half-life time in exotic ...

Indian Academy of Sciences (India)

Shi and Swiatecki [6] put forward a model for exotic decay studies that uses Coulomb and proximity potential as interacting barrier for post-scission region and uses simple power law for overlap region. These authors [7] studied the effect of deformation of parent, daughter and shell attenuation on half-life time treating ...

Proteomic profiles reveal age-related changes in coelomic fluid of sea urchin species with different life spans.

Science.gov (United States)

Bodnar, Andrea

2013-05-01

Sea urchins have a different life history from humans and traditional model organisms used to study the process of aging. Sea urchins grow indeterminately, reproduce throughout their life span and some species have been shown to exhibit negligible senescence with no increase in mortality rate at advanced ages. Despite these properties, different species of sea urchins are reported to have very different natural life spans providing a unique model to investigate cellular mechanisms underlying life span determination and negligible senescence. To gain insight into the biological changes that accompany aging in these animals, proteomic profiles were examined in coelomic fluid from young and old sea urchins of three species with different life spans: short-lived Lytechinus variegatus, long-lived Strongylocentrotus franciscanus and Strongylocentrotus purpuratus which has an intermediate life span. The proteomic profiles of cell-free coelomic fluid were complex with many proteins exhibiting different forms and extensive post-translational modifications. Approximately 20% of the protein spots on 2-D gels showed more than two-fold change with age in each of the species. Changes that are consistent with age in all three species may prove to be useful biomarkers for age-determination for these commercially fished marine invertebrates and also may provide clues to mechanisms of negligible senescence. Among the proteins that change with age, the ectodomain of low-density lipoprotein receptor-related protein 4 (LRP4) was significantly increased in the coelomic fluid of all three sea urchin species suggesting that the Wnt signaling pathway should be further investigated for its role in negligible senescence. Copyright © 2012 Elsevier Inc. All rights reserved.

Going Beyond the Binary : The body, Sexuality and Identity in Shelley Jackson’s Half Life: a novel

OpenAIRE

Liu, Linjing

2012-01-01

The thesis focuses on Shelley Jackson’s Half Life: a Novel with efforts directed towards a literary interpretation considering relevant issues within the context of gender and feminist theory. The argument rests upon four basic units: the theoretical framework at the outset, the question of the body next, thirdly an investigation of sexuality, and finally a consideration of identity. In Jackson’s Half Life: a Novel the non-dualist thinking underlies a deliberate play of dualism. To go beyond ...

Fenobody: A Ferritin-Displayed Nanobody with High Apparent Affinity and Half-Life Extension.

Science.gov (United States)

Fan, Kelong; Jiang, Bing; Guan, Zhe; He, Jiuyang; Yang, Dongling; Xie, Ni; Nie, Guohui; Xie, Can; Yan, Xiyun

2018-04-10

Nanobodies consist of a single domain variable fragment of a camelid heavy-chain antibody. Nanobodies have potential applications in biomedical fields because of their simple production procedures and low cost. Occasionally, nanobody clones of interest exhibit low affinities for their target antigens, which, together with their short half-life limit bioanalytical or therapeutic applications. Here, we developed a novel platform we named fenobody, in which a nanobody developed against H5N1 virus is displayed on the surface of ferritin in the form of a 24mer. We constructed a fenobody by substituting the fifth helix of ferritin with the nanobody. TEM analysis showed that nanobodies were displayed on the surface of ferritin in the form of 6 × 4 bundles, and that these clustered nanobodies are flexible for antigen binding in spatial structure. Comparing fenobodies with conventional nanobodies currently used revealed that the antigen binding apparent affinity of anti-H5N1 fenobody was dramatically increased (∼360-fold). Crucially, their half-life extension in a murine model was 10-fold longer than anti-H5N1 nanobody. In addition, we found that our fenobodies are highly expressed in Escherichia coli, and are both soluble and thermo-stable nanocages that self-assemble as 24-polymers. In conclusion, our results demonstrate that fenobodies have unique advantages over currently available systems for apparent affinity enhancement and half-life extension of nanobodies. Our fenobody system presents a suitable platform for various large-scale biotechnological processes and should greatly facilitate the application of nanobody technology in these areas.

Arabidopsis Regenerating Protoplast: A Powerful Model System for Combining the Proteomics of Cell Wall Proteins and the Visualization of Cell Wall Dynamics

Science.gov (United States)

Yokoyama, Ryusuke; Kuki, Hiroaki; Kuroha, Takeshi; Nishitani, Kazuhiko

2016-01-01

The development of a range of sub-proteomic approaches to the plant cell wall has identified many of the cell wall proteins. However, it remains difficult to elucidate the precise biological role of each protein and the cell wall dynamics driven by their actions. The plant protoplast provides an excellent means not only for characterizing cell wall proteins, but also for visualizing the dynamics of cell wall regeneration, during which cell wall proteins are secreted. It therefore offers a unique opportunity to investigate the de novo construction process of the cell wall. This review deals with sub-proteomic approaches to the plant cell wall through the use of protoplasts, a methodology that will provide the basis for further exploration of cell wall proteins and cell wall dynamics. PMID:28248244

Propose of a model for dose and hazard calculation due the Rn-222, Rn-220 and its short half-life daugthers inhalation

International Nuclear Information System (INIS)

Mauricio, C.L.P.

1982-01-01

The compartimental dosimetric model is used to simulate, by computer, the interactions of the inhalated radon atom radiations and its short half-life daugthers with cells. The metabolic trajectory of these radionuclides is described by differential equations of continuous medium dynamics, where the elements transform by radioactive decay. This work permits to determine the individual retenction function, beeing useful in radioprotection routines or emergence situations. The results of internal dosimetry are consistent with the new I.C.R.P. - 32 international recommendations. (L.C.) [pt

Doubling and half-life times for a combined fission-fusion system

Energy Technology Data Exchange (ETDEWEB)

Pantis, G

1982-01-01

The long term fuel dynamics for a fission symbiotic system is examined under the assumption of discontinuous loading and offloading conditions. It is found that the breeding capacities of the core and the blankets identify several distinct fuel cycles. By numerical test and a specific comparison it is shown that doubling times and half-lives can differ by as much as 10% from those predicted by conventional methods.

Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment.

Science.gov (United States)

Welker, F

2018-02-20

The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As a result, peptide and protein identification rates are higher in error-tolerant mode compared to non-error-tolerant searches but did not recover protein identifications completely. Data indicates that peptide length and the number of mutations between the target and database sequences are the main factors influencing mutable PSM identification. The error-tolerant results suggest that the cross-species proteomics problem is not overcome at increasing evolutionary distances, even at the protein level. Peptide and protein loss has the potential to significantly impact divergence dating and proteome comparisons when using ancient samples as there is a bias towards the identification of conserved sequences and proteins. Effects are minimized

Improved half-life determination and β-delayed γ-ray spectroscopy for 18Ne decay

Science.gov (United States)

Grinyer, G. F.; Ball, G. C.; Bouzomita, H.; Ettenauer, S.; Finlay, P.; Garnsworthy, A. B.; Garrett, P. E.; Green, K. L.; Hackman, G.; Leslie, J. R.; Pearson, C. J.; Rand, E. T.; Sumithrarachchi, C. S.; Svensson, C. E.; Thomas, J. C.; Triambak, S.; Williams, S. J.

2013-04-01

The half-life of the superallowed Fermi β+ emitter 18Ne has been determined to ±0.07% precision by counting 1042 keV delayed γ rays that follow approximately 8% of all β decays. The deduced half-life, T1/2=1.6648(11) s, includes a 0.7% correction that accounts for systematic losses associated with rate-dependent detector pulse pileup that was determined using a recently developed γ-ray photopeak-counting technique. This result is a factor of two times more precise than, and in excellent agreement with, a previous lower-statistics measurement that employed the same experimental setup. High-resolution β-delayed γ-ray spectroscopy results for the relative γ-ray intensities and β-decay branching ratios to excited states in the daughter 18F are also presented.

The proteome of human saliva

Science.gov (United States)

Griffin, Timothy J.

2013-05-01

Human saliva holds tremendous potential for transforming disease and health diagnostics given its richness of molecular information and non-invasive collection. Enumerating its molecular constituents is an important first step towards reaching this potential. Among the molecules in saliva, proteins and peptides arguably have the most value: they can directly indicate biochemical functions linked to a health condition/disease state, and they are attractive targets for biomarker assay development. However, cataloging and defining the human salivary proteome is challenging given the dynamic, chemically heterogeneous and complex nature of the system. In addition, the overall human saliva proteome is composed of several "sub-proteomes" which include: intact full length proteins, proteins carrying post-translational modifications (PTMs), low molecular weight peptides, and the metaproteome, derived from protein products from nonhuman organisms (e.g. microbes) present in the oral cavity. Presented here will be a summary of communal efforts to meet the challenge of characterizing the multifaceted saliva proteome, focusing on the use of mass spectrometry as the proteomic technology of choice. Implications of these efforts to characterize the salivary proteome in the context of disease diagnostics will also be discussed.

The Monkey King: a personal view of the long journey towards a proteomic Nirvana.

Science.gov (United States)

Righetti, Pier Giorgio

2014-07-31

The review covers about fifty years of progress in "proteome" analysis, starting from primitive two-dimensional (2D) map attempts in the early sixties of last century. The polar star in 2D mapping arose in 1975 with the classic paper by O'Farrell in J Biol. Chem. It became the compass for all proteome navigators. Perfection came, though, only with the introduction of immobilized pH gradients, which fixed the polypeptide spots in the 2D plane. Great impetus in proteome analysis came with the introduction of informatic tools and creating databases, among which Swiss Prot remains the site of excellence. Towards the end of the nineties, 2D chromatography, epitomized by coupling strong cation exchangers with C18 resins, began to be a serious challenge to electrophoretic 2D mapping, although up to the present both techniques are still much in vogue and appear to give complementary results. Yet the migration of "proteomics" into the third millennium was made possible only by mass spectrometry (MS), which today represents the standard analytical tool in any lab dealing with proteomic analysis. Another major improvement has been the introduction of combinatorial peptide ligand libraries (CPLL), which, when properly used, enhance the visibility of low-abundance species by 3 to 4 orders of magnitude. Coupling MS to CPLLs permits the exploration of at least 8 orders of magnitude in dynamic range on any proteome. The present review is a personal recollection highlighting the developments that led to present-day proteomics on a long march that lasted about 50years. It is meant to give to young scientists an overview on how science grows, which ones are the quantum jumps in science and which research is of particular significance in general and in the field of proteomics in particular. It also gives some real-life episodes of greater-than-life figures. As such, it can be viewed as a tutorial to stimulate the young generation to be creative (and use their imagination too

Safety and Efficacy of BAY 94-9027, a Prolonged-Half-Life Factor VIII

DEFF Research Database (Denmark)

Reding, M T; Ng, H J; Poulsen, Lone Hvitfeldt

2017-01-01

BACKGROUND: BAY 94-9027 is a B-domain-deleted prolonged-half-life recombinant factor VIII (FVIII) conjugates in a site-specific manner with polyethylene glycol. OBJECTIVE: Assess efficacy and safety of BAY 94-9027 for prophylaxis and treatment of bleeds in patients with severe hemophilia A PATIEN...

Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Science.gov (United States)

Van, Phu T; Schmid, Amy K; King, Nichole L; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T; Goo, Young Ah; Deutsch, Eric W; Reiss, David J; Mallick, Parag; Baliga, Nitin S

2008-09-01

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Vortex and half-vortex dynamics in a nonlinear spinor quantum fluid.

Science.gov (United States)

Dominici, Lorenzo; Dagvadorj, Galbadrakh; Fellows, Jonathan M; Ballarini, Dario; De Giorgi, Milena; Marchetti, Francesca M; Piccirillo, Bruno; Marrucci, Lorenzo; Bramati, Alberto; Gigli, Giuseppe; Szymańska, Marzena H; Sanvitto, Daniele

2015-12-01

Vortices are archetypal objects that recur in the universe across the scale of complexity, from subatomic particles to galaxies and black holes. Their appearance is connected with spontaneous symmetry breaking and phase transitions. In Bose-Einstein condensates and superfluids, vortices are both point-like and quantized quasiparticles. We use a two-dimensional (2D) fluid of polaritons, bosonic particles constituted by hybrid photonic and electronic oscillations, to study quantum vortex dynamics. Polaritons benefit from easiness of wave function phase detection, a spinor nature sustaining half-integer vorticity, strong nonlinearity, and tuning of the background disorder. We can directly generate by resonant pulsed excitations a polariton condensate carrying either a full or half-integer vortex as initial condition and follow their coherent evolution using ultrafast imaging on the picosecond scale. The observations highlight a rich phenomenology, such as the spiraling of the half-vortex and the joint path of the twin charges of a full vortex, until the moment of their splitting. Furthermore, we observe the ordered branching into newly generated secondary couples, associated with the breaking of radial and azimuthal symmetries. This allows us to devise the interplay of nonlinearity and sample disorder in shaping the fluid and driving the vortex dynamics. In addition, our observations suggest that phase singularities may be seen as fundamental particles whose quantized events span from pair creation and recombination to 2D+t topological vortex strings.

High-precision half-life measurements for the superallowed Fermi β+ emitter 14O

Science.gov (United States)

Laffoley, A. T.; Svensson, C. E.; Andreoiu, C.; Austin, R. A. E.; Ball, G. C.; Blank, B.; Bouzomita, H.; Cross, D. S.; Diaz Varela, A.; Dunlop, R.; Finlay, P.; Garnsworthy, A. B.; Garrett, P. E.; Giovinazzo, J.; Grinyer, G. F.; Hackman, G.; Hadinia, B.; Jamieson, D. S.; Ketelhut, S.; Leach, K. G.; Leslie, J. R.; Tardiff, E.; Thomas, J. C.; Unsworth, C.

2013-07-01

The half-life of the superallowed Fermi β+ emitter 14O has been determined via simultaneous direct β and γ counting experiments at TRIUMF's Isotope Separator and Accelerator (ISAC) facility. A γ-ray counting measurement was performed by detecting the 2312.6-keV γ rays emitted from an excited state of the daughter 14N following the implantation of samples at the center of the 8π γ-ray spectrometer, a spherical array of 20 high-purity germanium (HPGe) detectors. A simultaneous β counting experiment was performed using a fast plastic scintillator positioned behind the implantation site with a solid angle coverage of ˜20%. The results, T1/2(β)=70.610±0.030s and T1/2(γ)=70.632±0.094s, form a consistent set and, together with eight previous measurements, establish a new average for the 14O half-life of T1/2=70.619±0.011s with a reduced χ2 of 0.99.

Dissecting the C. elegans response during infection using quantitative proteomics

DEFF Research Database (Denmark)

Simonsen, Karina Trankjær; Møller-Jensen, Jakob; Kristensen, Anders Riis

2008-01-01

The adherent invasive E. coli isolated from patients with Crohn’s disease in humans is pathogenic for C. elegans. We show here that when C. elegans feeds on the pathogenic E. coli, the life span is shortened significantly compared to the normal laboratory food, the OP50 E. coli. In this study...... the infection process is followed using GFP-expressing bacteria and persistence assays. A quantitative proteomic approach was used to follow the C. elegans host response during the infection process. C. elegans were metabolic labeled with the stable isotope 15N and samples from three different time points......, many of which also have been found in studies using other pathogens. So far, large-scale investigations of the C. elegans immune response have been performed using micro-arrays. This study is the first to make use of quantitative proteomics to directly follow the protein dynamics during the infection...

Arabidopsis peroxisome proteomics

Directory of Open Access Journals (Sweden)

John D. Bussell

2013-04-01

Full Text Available The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. This is primarily due to the difficulties associated with isolating and obtaining purified samples of peroxisomes from Arabidopsis. So far only a handful of research groups have been successful in obtaining such fractions. To make things worse, enriched peroxisome fractions frequently suffer from significant organellar contamination, lowering confidence in localization assignment of the identified proteins. As with other cellular compartments, identification of peroxisomal proteins forms the basis for investigations of the dynamics of the peroxisomal proteome. It is therefore not surprising that, in terms of functional analyses by proteomic means, there remains a considerable gap between peroxisomes and chloroplasts or mitochondria. Alternative strategies are needed to overcome the obstacle of hard-to-obtain organellar fractions. This will help to close the knowledge gap between peroxisomes and other organelles and provide a full picture of the physiological pathways shared between organelles. In this review we briefly summarize the status quo and discuss some of the methodological alternatives to classic organelle proteomic approaches.

The Half-Life of the HSV-1 1.5 kb LAT Intron is similar to the half-Life of the 2.0 kb LAT Intron

Science.gov (United States)

Brinkman, Kerry K.; Mishra, Prakhar; Fraser, Nigel W.

2013-01-01

Herpes Simplex Virus type 1 (HSV-1) establishes a latent infection in the sensory neurons of the peripheral nervous system of humans. Although about 80 genes are expressed during the lytic cycle of the virus infection, essentially only one gene is expressed during the latent cycle. This gene is known as the latency associated transcript (LAT) and it appears to play a role in the latency cycle through an anti-apoptotic function in the 5’ end of the gene and miRNA encoded along the length of the transcript which down regulate some of the viral immediate early (IE) gene products. The LAT gene is about 8.3 kb long and consists of two exons separated by an unusual intron. The intron between the exons consists of two nested introns. This arrangement of introns has been called a twintron. Furthermore, the larger (2 kb) intron has been shown to be very stable. In this study we measure the stability of the shorter 1.5 kb nested intron and find its half-life is similar to the longer intron. This was achieved by deleting the 0.5 kb overlapping intron from a plasmid construct designed to express the LAT transcript from a tet-inducible promoter, and measuring the half-life of the 1.5 kb intron in tissue culture cells. This finding supports the hypothesis that it is the common branch-point region of these nested introns that is responsible for their stability. PMID:23335177

Hour Glass Half-Full or Half-Empty? Future Time Perspective and Preoccupation with Negative Events Across the Life Span

Science.gov (United States)

Strough, JoNell; de Bruin, Wändi Bruine; Parker, Andrew M.; Lemaster, Philip; Pichayayothin, Nipat; Delaney, Rebecca

2016-01-01

According to socioemotional selectivity theory, older adults' emotional well-being stems from having limited future time perspective that motivates them to maximize well-being in the “here and now.” Presumably, then, older adults' time horizons are associated with emotional competencies that boost positive affect and dampen negative affect, but little research has addressed this. Using a US national adult life-span sample (N= 3,933, 18-93 yrs), we found that a two-factor model of future time perspective (focus on future opportunities; focus on limited time) fit the data better than a one-factor model. Through middle age, people perceived the life-span hourglass as half full—they focused more on future opportunities than limited time. Around age 60, the balance changed to increasingly perceiving the life-span hourglass as half empty—they focused less on future opportunities and more on limited time. This pattern held even after accounting for perceived health, self-reported decision-making ability, and retirement status. At all ages, women's time horizons focused more on future opportunities compared to men's, and men's focused more on limited time. Focusing on future opportunities was associated with reporting less preoccupation with negative events, whereas focusing on limited time was associated with reporting more preoccupation. Older adults reported less preoccupation with negative events and this association was stronger after controlling for their perceptions of limited time and fewer future opportunities, suggesting that other pathways may explain older adults' reports of their ability to disengage from negative events. Insights gained and questions raised by measuring future time perspective as two dimensions are discussed. PMID:27267222

Hour glass half full or half empty? Future time perspective and preoccupation with negative events across the life span.

Science.gov (United States)

Strough, JoNell; Bruine de Bruin, Wändi; Parker, Andrew M; Lemaster, Philip; Pichayayothin, Nipat; Delaney, Rebecca

2016-09-01

According to socioemotional selectivity theory, older adults' emotional well-being stems from having a limited future time perspective that motivates them to maximize well-being in the "here and now." Presumably, then, older adults' time horizons are associated with emotional competencies that boost positive affect and dampen negative affect, but little research has addressed this. Using a U.S. adult life-span sample (N = 3,933; 18-93 years), we found that a 2-factor model of future time perspective (future opportunities; limited time) fit the data better than a 1-factor model. Through middle age, people perceived the life-span hourglass as half full-they focused more on future opportunities than limited time. Around Age 60, the balance changed to increasingly perceiving the life-span hourglass as half empty-they focused less on future opportunities and more on limited time, even after accounting for perceived health, self-reported decision-making ability, and retirement status. At all ages, women's time horizons focused more on future opportunities compared with men's, and men's focused more on limited time. Focusing on future opportunities was associated with reporting less preoccupation with negative events, whereas focusing on limited time was associated with reporting more preoccupation. Older adults reported less preoccupation with negative events, and this association was stronger after controlling for their perceptions of limited time and fewer future opportunities, suggesting that other pathways may explain older adults' reports of their ability to disengage from negative events. Insights gained and questions raised by measuring future time perspective as 2 dimensions are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Dynamic Proteomics Emphasizes the Importance of Selective mRNA Translation and Protein Turnover during Arabidopsis Seed Germination*

Science.gov (United States)

Galland, Marc; Huguet, Romain; Arc, Erwann; Cueff, Gwendal; Job, Dominique; Rajjou, Loïc

2014-01-01

During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [35S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment. PMID:24198433

Precise half-life measurement of the superallowed β+ emitter 38Km

International Nuclear Information System (INIS)

Ball, G. C.; Boisvert, G.; Bricault, P.; Churchman, R.; Dombsky, M.; Lindner, T.; Macdonald, J. A.; Vandervoort, E.; Bishop, S.; D'Auria, J. M.; Hardy, J. C.; Iacob, V. E.; Leslie, J. R.; Mak, H.-B.

2010-01-01

The half-life of 38 K m has been measured to be 924.46(14) ms, a result that is a factor of two more precise than any of the five previous measurements of this quantity. The previous results are not consistent with one another, but our result agrees well with the two most recent ones. The derived ft value for 38 K m is now one of the three most precisely known superallowed ft values.

Label-free Fab and Fc affinity/avidity profiling of the antibody complex half-life for polyclonal and monoclonal efficacy screening.

Science.gov (United States)

Read, Thomas; Olkhov, Rouslan V; Williamson, E Diane; Shaw, Andrew M

2015-09-01

A unified approach to affinity screening for Fab and Fc interactions of an antibody for its antigen and FcγR receptor has been developed. An antigen array is used for the Fab affinity and cross-reactivity screening and protein A/G proxy is the FcγR receptor. The affinities are derived using a simple 1:1 binding model with a consistent error analysis. The association and dissociation kinetics are measured over optimised times for accurate determination. The Fab/Fc affinities are derived for ten antibodies: mAb-actin (mouse), pAb-BSA (sheep), pAb-collagen V (rabbit), pAb-CRP (goat), mAb-F1 (mouse), mAbs (mouse) 7.3, 12.3, 29.3, 36.3 and 46.3 raised against LcrV in Yersinia pestis. The rate of the dissociation of antigen-antibody complexes relates directly to their immunological function as does the Fc-FcγR complex and a new half-life plot has been defined with a Fab/Fc half-life range of 17-470 min. The upper half-life value points to surface avidity. Two antibodies that are protective as an immunotherapy define a Fab half-life >250 min and an Fc half-life >50 min as characteristics of ideal interactions which can form the basis of an antibody screen for immunotherapy.

Examination of the biological half-life and organ d;stribution of tritiated lysin-vasopressin in Brattleboro rats

International Nuclear Information System (INIS)

Laczi, F.; Laszlo, F.

1980-01-01

15 μCi tritiated lysin-vasopressin (spec. act. 3.5 Ci per mmol) was administered to control and Brattleboro rats, suffering from hereditary hypothalamic diabetes insipidus. The biological half-life and the distribution of the labelled compound in the different organs were determined. The biological half-life demonstrated no significant difference, however, the vasopressin content of the small intestine was higher in the Brattleboro rats. In the other organs no significant difference was found. It can be concluded that the hereditary diabetes insipidus is not due to faster elimination of circulating vasopressin. (L.E.)

Examination of the biological half-life and organ d; stribution of tritiated lysin-vasopressin in Brattleboro rats

Energy Technology Data Exchange (ETDEWEB)

Laczi, F; Laszlo, F [Szegedi Orvostudomanyi Egyetem Szeged (Hungary). 1. Belgyogyaszati Klinika; Keri, Gy; Teplan, I [Semmelweis Orvostudomanyi Egyetem, Budapest (Hungary)

1980-04-01

15 ..mu..Ci tritiated lysin-vasopressin (spec. act. 3.5 Ci per mmol) was administered to control and Brattleboro rats, suffering from hereditary hypothalamic diabetes insipidus. The biological half-life and the distribution of the labelled compound in the different organs were determined. The biological half-life demonstrated no significant difference, however, the vasopressin content of the small intestine was higher in the Brattleboro rats. In the other organs no significant difference was found. It can be concluded that the hereditary diabetes insipidus is not due to faster elimination of circulating vasopressin.

High-Precision Half-Life Measurements for the Superallowed Fermi β+ Emitters 14O and 18Ne

Science.gov (United States)

Laffoley, A. T.; Andreoiu, C.; Austin, R. A. E.; Ball, G. C.; Bender, P. C.; Bidaman, H.; Bildstein, V.; Blank, B.; Bouzomita, H.; Cross, D. S.; Deng, G.; Diaz Varela, A.; Dunlop, M. R.; Dunlop, R.; Finlay, P.; Garnsworthy, A. B.; Garrett, P.; Giovinazzo, J.; Grinyer, G. F.; Grinyer, J.; Hadinia, B.; Jamieson, D. S.; Jigmeddorj, B.; Ketelhut, S.; Kisliuk, D.; Leach, K. G.; Leslie, J. R.; MacLean, A.; Miller, D.; Mills, B.; Moukaddam, M.; Radich, A. J.; Rajabali, M. M.; Rand, E. T.; Svensson, C. E.; Tardiff, E.; Thomas, J. C.; Turko, J.; Voss, P.; Unsworth, C.

High-precision half-life measurements, at the level of ±0.04%, for the superallowed Fermi emitters 14O and 18Ne have been performed at TRIUMF's Isotope Separator and Accelerator facility. Using 3 independent detector systems, a gas-proportional counter, a fast plastic scintillator, and a high-purity germanium array, a series of direct β and γ counting measurements were performed for each of the isotopes. In the case of 14O, these measurements were made to help resolve an existing discrepancy between detection methods, whereas for 18Ne the half-life precision has been improved in anticipation of forthcoming high-precision branching ratio measurements.

Comparison of isotope dilution and excretion methods for determining the half-life of ascorbic acid in the guinea pig

International Nuclear Information System (INIS)

Kipp, D.E.; Rivers, J.M.

1984-01-01

The half-life of ascorbic acid (AA) in guinea pigs was investigated by the isotope dilution and excretion methods. The dilution method measures [1-14C]AA disappearance from the plasma, whereas the excretion method measures the elimination of [1-14C]AA and the metabolites from the body. Two groups of animals underwent both isotope studies in reverse order. Animals were conditioned to the experimental procedures and fed 2.5 mg AA/100 g body weight orally to maintain a daily intake of the vitamin independent of food consumption. The two isotope procedures imposed similar stress on the animals, as determined by plasma cortisol levels and body weight changes. The AA half-life calculations of the rapidly exchangeable pool by the isotope dilution method yielded values of 1.23 and 0.34 hours for the two groups, respectively. The half-life of the slowly exchangeable pool for the two groups was 60.2 and 65.8 hours, respectively. The half-life of AA in the rapidly exchangeable pool, as measured by the excretion studies, was 4.57-8.75 hours. For the slowly exchangeable pool, it was 146-149 hours. The longer half-life of both pools obtained with the excretion method indicates that the isotope is disappearing from the plasma more rapidly than it is being excreted. This suggests that a portion of the [1-14C]AA leaving the plasma is removed to a body pool that is not sampled by the isotope excretion method

Towards a measurement of the half-life of {sup 60}Fe for stellar and early Solar System models

Energy Technology Data Exchange (ETDEWEB)

Ostdiek, K.; Anderson, T. [University of Notre Dame, Notre Dame, IN 46556 (United States); Bauder, W. [University of Notre Dame, Notre Dame, IN 46556 (United States); Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439 (United States); Bowers, M.; Collon, P. [University of Notre Dame, Notre Dame, IN 46556 (United States); Dressler, R. [Paul Scherrer Institute – Laboratory for Radiochemistry and Environmental Chemistry, 5232 Villigen (Switzerland); Greene, J. [Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439 (United States); Kutschera, W. [Vienna Environmental Research Accelerator Laboratory, Waehringer Strasse 17, 1090 Vienna (Austria); Lu, W. [University of Notre Dame, Notre Dame, IN 46556 (United States); Paul, M. [Racah Institute of Physics, Hebrew University, Jerusalem 91904 (Israel); Robertson, D. [University of Notre Dame, Notre Dame, IN 46556 (United States); Schumann, D. [Paul Scherrer Institute – Laboratory for Radiochemistry and Environmental Chemistry, 5232 Villigen (Switzerland); Skulski, M. [University of Notre Dame, Notre Dame, IN 46556 (United States); Wallner, A. [The Australian National University, Canberra, ACT 0200 (Australia)

2015-10-15

Radioisotopes, produced in stars and ejected into the Interstellar Medium, are important for constraining stellar and early Solar System (ESS) models. In particular, the half-life of the radioisotope, {sup 60}Fe, can have an impact on calculations for the timing for ESS events, the distance to nearby Supernovae, and the brightness of individual, non-steady-state {sup 60}Fe gamma ray sources in the Galaxy. A half-life measurement has been undertaken at the University of Notre Dame and measurements of the {sup 60}Fe/{sup 56}Fe concentration of our samples using Accelerator Mass Spectrometry has begun. This result will be coupled with an activity measurement of the isomeric decay in {sup 60}Co, which is the decay product of {sup 60}Fe. Preliminary half-life estimates of (2.53 ± 0.24) × 10{sup 6} years seem to confirm the recent measurement by Rugel et al. (2009).

Half-life, branching-ratio, and Q-value measurement for the superallowed 0+→0+β+ emitter 42Ti

International Nuclear Information System (INIS)

Nieto, T. Kurtukian; Souin, J.; Audirac, L.; Blank, B.; Giovinazzo, J.; Eronen, T.; Aeystoe, J.; Elomaa, V.-V.; Hager, U.; Hakala, J.; Jokinen, A.; Kankainen, A.; Karvonen, P.; Kessler, T.; Moore, I. D.; Penttilae, H.; Rahaman, S.; Reponen, M.; Rissanen, J.; Saastamoinen, A.

2009-01-01

The half-life, the branching ratio, and the decay Q value of the superallowed β emitter 42 Ti were measured in an experiment performed at the JYFLTRAP facility of the Accelerator Laboratory of the University of Jyvaeskylae. 42 Ti is the heaviest T z =-1 nucleus for which high-precision measurements of these quantities have been tried. The half-life (T 1/2 =208.14±0.45 ms) and the Q value [Q EC =7016.83(25) keV] are close to or reach the required precision of about 0.1%. The branching ratio for the superallowed decay branch [BR=47.7(12)%], a by-product of the half-life measurement, does not reach the necessary precision yet. Nonetheless, these results allow one to determine the experimental ft value and the corrected Ft value to be 3114(79) and 3122(79) s, respectively.

Dynamics of nuclear matrix proteome during embryonic ...

Indian Academy of Sciences (India)

stage (14–16 h) NuMat proteome in functional group X, CS>0 .... Indicates % of proteins in the corresponding class that vary between the age group embryos. ..... (GO) classification based on molecular functions, biological ... toys are us.

Tests of the methods of analysis of picosecond lifetimes and measurement of the half-life of the 569.6 keV level in 207Pb

International Nuclear Information System (INIS)

Lima, E. de; Kawakami, H.; Lima, A. de; Hichwa, R.; Ramayya, A.V.; Hamilton, J.H.; Dunn, W.; Kim, H.J.

1978-01-01

Customarily one extracts the half-life of the nuclear state from a delayed time spectrum by an analysis of the centroid shift, the slope and lately by the convolution method. Recently there have been two formulas relating the centroid shift to the half-life of the nuclear state. These two procedures can give different results for the half-life when Tsub(1/2) the same order or less than the time width of one channel. An extensive investigation of these two formulas and precedures has been made by measuring the half-life of the first excited state in 207 Pb at 569.6 keV. This analysis confirms Bay's formula relating the centroid shift to the half-life of the state. The half-life of the 569.6 keV level in 207 Pb is measured to be (129+-3) ps in excellent agreement with Weisskopf's single particle estimate of 128 ps for an E2 transition. (Auth.)

Measurements of Actual Effective Half - Life in {sup 131}I Therapy for Graves' Hyperthyroidism

Energy Technology Data Exchange (ETDEWEB)

So, Yong Seon; Kim, Myung Seon; Kwon, Ki Hyun; Kim, Seok Whan; Kim, Tae Hyung; Han, Sang Woong; Kim, Eun Sil; Kim, Chong Soon [Hanil General Hospital, Seoul (Korea, Republic of)

1996-03-15

Radioiodine[131I] has been used for the treatment of Graves' hyperthyroidism since the late 1940's and is now generally regarded as the treatment of choice for Graves' hyperthyroidism who does not remit following a course of antithyroid drugs. But for the dose given, several different protocols have been described by different centers, each attempting to reduce the incidence of long-term hypothyroidism while maintaining an acceptable rate control of Graves' hyperthyroidism. Our goals were to evaluate effective half-life and predict absorbed dose in Graves' hyperthyroidism patients, therefore, to calculate and read minister radioiodine activity needed to achieve aimed radiation dose. Our data showed that the mean effective 131I half-life for Graves' disease is 5.3 days(S.D=0.88) and mean biologic half-life is 21 days, range 9.5-67.2 days. The mean administered activity and the mean values of absorbed doses wet: 532 MBq(S.D.=254), 112 Gy (S.D.=50.9), respectively. The mean activity needed to achieve aimed radiation dose were 51 MBq and marked differences of 131I thyroidal uptake between tracer and therapy occurred in our study. We are sure that the dose calculation method that uses 5 days thyroidal 131I uptake measurements after tracer and therapy dose, provides sufficient data about the effective treatment in Graves' hyperthyroidism.

Usefulness of analytical CEA doubling time and half-life time for overlooked synchronous metastases in colorectal carcinoma.

Science.gov (United States)

Ito, Katsuki; Hibi, Kenji; Ando, Hideyuki; Hidemura, Kazuhiko; Yamazaki, Taiji; Akiyama, Seiji; Nakao, Akimasa

2002-02-01

Measurement of carcinoembryonic antigen (CEA) has been widely applied to detect recurrence, especially of colorectal carcinoma. The validity however, is still controversial. We investigated serial changes in CEA values to calculate whether the CEA doubling time and half-life time could predict metastatic progression or prognosis in colorectal carcinoma. Pre- and post-operative serial serum CEA contents were determined in 22 cases of colorectal cancer with or without metastasis. CEA values were determined by enzyme immunoassay (EIA). Patients were assigned depending upon survival time (within vs. more than 18 months after primary resection) for assessment of CEA doubling time. From the gradient of the semi-logarithmic CEA graph, the preoperative doubling time was calculated and the postoperative half-life time was estimated according to the diagnosis of metastases within 2 years after primary resection [metastasis (+) or (-)]. In spite of the effect of curative re-operation of metastatic lesions or of postoperative adjuvant chemotherapy, the CEA doubling time of the groups showed a relation with prognosis (p = 0.045, Student's t-test) when the patients were divided into >18 and time. The CEA half-life time of the groups without overlooked metastases was statistically longer than those with (mean +/- SD 8.01 +/- 2.07 and 4.33 +/- 1.11, respectively, p Clearance (k) showed a significant difference between the groups (p time appeared to be a less independent prognostic factor, whereas prolongation of the CEA half-life time might potentially suggest the existence of overlooked synchronous metastases from colorectal carcinoma.

Red blood cell (RBC) membrane proteomics--Part I: Proteomics and RBC physiology.

Science.gov (United States)

Pasini, Erica M; Lutz, Hans U; Mann, Matthias; Thomas, Alan W

2010-01-03

Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of nucleus and organelles in mammalian species other than camelids, and constantly in motion in the blood stream, red blood cells (RBCs) are the sole mammalian oxygen transporter. The fact that mature mammalian RBCs have no internal membrane-bound organelles, somewhat simplifies proteomics analysis of the plasma membrane and the fact that it has no nucleus disqualifies microarray based methods. Proteomics has the potential to provide a better understanding of this critical interface, and thereby assist in identifying new approaches to diseases. (c) 2009 Elsevier B.V. All rights reserved.

Hardy inequality on time scales and its application to half-linear dynamic equations

Directory of Open Access Journals (Sweden)

Řehák Pavel

2005-01-01

Full Text Available A time-scale version of the Hardy inequality is presented, which unifies and extends well-known Hardy inequalities in the continuous and in the discrete setting. An application in the oscillation theory of half-linear dynamic equations is given.

Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study

OpenAIRE

Sun, Su; Xie, Shangxian; Cheng, Yanbing; Yu, Hongbo; Zhao, Honglu; Li, Muzi; Li, Xiaotong; Zhang, Xiaoyu; Yuan, Joshua S.; Dai, Susie Y.

2017-01-01

Proteomics studies of fungal systems have progressed dramatically based on the availability of more fungal genome sequences in recent years. Different proteomics strategies have been applied toward characterization of fungal proteome and revealed important gene functions and proteome dynamics. Presented here is the application of shot-gun proteomic technology to study the bio-remediation of environmental hazards by white-rot fungus. Lignin, a naturally abundant component of the plant biomass,...

Ultra-High Precision Half-Life Measurement for the Superallowed &+circ; Emitter ^26Al^m

Science.gov (United States)

Finlay, P.; Demand, G.; Garrett, P. E.; Leach, K. G.; Phillips, A. A.; Sumithrarachchi, C. S.; Svensson, C. E.; Triambak, S.; Grinyer, G. F.; Leslie, J. R.; Andreoiu, C.; Cross, D.; Austin, R. A. E.; Ball, G. C.; Bandyopadhyay, D.; Djongolov, M.; Ettenauer, S.; Hackman, G.; Pearson, C. J.; Williams, S. J.

2009-10-01

The calculated nuclear structure dependent correction for ^26Al^m (δC-δNS= 0.305(27)% [1]) is smaller by nearly a factor of two than the other twelve precision superallowed cases, making it an ideal case to pursue a reduction in the experimental errors contributing to the Ft value. An ultra-high precision half-life measurement for the superallowed &+circ; emitter ^26Al^m has been made at the Isotope Separator and Accelerator (ISAC) facility at TRIUMF in Vancouver, Canada. A beam of ˜10^5 ^26Al^m/s was delivered in October 2007 and its decay was observed using a 4π continuous gas flow proportional counter as part of an ongoing experimental program in superallowed Fermi β decay studies. With a statistical precision of ˜0.008%, the present work represents the single most precise measurement of any superallowed half-life to date. [4pt] [1] I.S. Towner and J.C. Hardy, Phys. Rev. C 79, 055502 (2009).

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

Science.gov (United States)

Omenn, Gilbert S; Lane, Lydie; Lundberg, Emma K; Overall, Christopher M; Deutsch, Eric W

2017-12-01

The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 "missing proteins" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.

Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics

DEFF Research Database (Denmark)

Sidoli, Simone; Vandamme, Julien; Elisabetta Salcini, Anna

2016-01-01

We applied a middle-down proteomics strategy for large scale protein analysis during in vivo development of Caenorhabditis elegans. We characterized post-translational modifications (PTMs) on histone H3 N-terminal tails at eight time points during the C. elegans lifecycle, including embryo, larval......-occurring PTMs. We measured temporally distinct combinatorial PTM profiles during C. elegans development. We show that the doubly modified form H3K23me3K27me3, which is rare or non-existent in mammals, is the most abundant PTM in all stages of C. elegans lifecycle. The abundance of H3K23me3 increased during...... that is transmitted during dauer formation. Collectively, our data describe the dynamics of histone H3 combinatorial code during C. elegans lifecycle and demonstrate the feasibility of using middle-down proteomics to study in vivo development of multicellular organisms. This article is protected by copyright. All...

A Half-Life Measurement of the 343.4 keV Level in {sup 175}Lu

Energy Technology Data Exchange (ETDEWEB)

Hoejeberg, M; Malmskog, S G

1969-05-15

Great theoretical interest has recently been shown in the asymptotically forbidden 5/2 5/2+ [402] - 7/2 7/2+ [404] M1-transitions in {sup 181}Ta and {sup 175}Lu . Half-lives of the 5/2 5/2+ [402] level in {sup 175}Lu have been reported which differ by more than a factor of 10. Using an electron-electron coincidence spectrometer the half-life of this level has been re-measured and a value of (0.26 {+-} 0.02) nsec has been established.

Proteomic profile of acute myeloid leukaemia: A review update ...

African Journals Online (AJOL)

This review draws attention to the progress and advancements in cancer proteomics technology with the aim of simplifying the understanding of the mechanisms underlying the disease and to contribute to detection of biomarkers in addition to the development of novel treatments. Given that proteome is a dynamic entity of ...

Dependence of the half-life of ²²¹Fr on the implantation environment

DEFF Research Database (Denmark)

Olaizola, B.; Fraile, L.M.; Riisager, Karsten

2010-01-01

The possible dependence of the half-life of 221Fr on the solid-state environment has been investigated by the simultaneous measurement of implanted 221Fr ions in an insulator (Si) and a metallic substrate (Au) at the ISOLDE facility at CERN. Our results indicate that, if existing, the difference ...

Technological advances for deciphering the complexity of psychiatric disorders: merging proteomics with cell biology.

Science.gov (United States)

Wesseling, Hendrik; Guest, Paul C; Lago, Santiago G; Bahn, Sabine

2014-08-01

Proteomic studies have increased our understanding of the molecular pathways affected in psychiatric disorders. Mass spectrometry and two-dimensional gel electrophoresis analyses of post-mortem brain samples from psychiatric patients have revealed effects on synaptic, cytoskeletal, antioxidant and mitochondrial protein networks. Multiplex immunoassay profiling studies have found alterations in hormones, growth factors, transport and inflammation-related proteins in serum and plasma from living first-onset patients. Despite these advances, there are still difficulties in translating these findings into platforms for improved treatment of patients and for discovery of new drugs with better efficacy and side effect profiles. This review describes how the next phase of proteomic investigations in psychiatry should include stringent replication studies for validation of biomarker candidates and functional follow-up studies which can be used to test the impact on physiological function. All biomarker candidates should now be tested in series with traditional and emerging cell biological approaches. This should include investigations of the effects of post-translational modifications, protein dynamics and network analyses using targeted proteomic approaches. Most importantly, there is still an urgent need for development of disease-relevant cellular models for improved translation of proteomic findings into a means of developing novel drug treatments for patients with these life-altering disorders.

Proteomics in uveal melanoma.

LENUS (Irish Health Repository)

Ramasamy, Pathma

2014-01-01

Uveal melanoma is the most common primary intraocular malignancy in adults, with an incidence of 5-7 per million per year. It is associated with the development of metastasis in about 50% of cases, and 40% of patients with uveal melanoma die of metastatic disease despite successful treatment of the primary tumour. The survival rates at 5, 10 and 15 years are 65%, 50% and 45% respectively. Unlike progress made in many other areas of cancer, uveal melanoma is still poorly understood and survival rates have remained similar over the past 25 years. Recently, advances made in molecular genetics have improved our understanding of this disease and stratification of patients into low risk and high risk for developing metastasis. However, only a limited number of studies have been performed using proteomic methods. This review will give an overview of various proteomic technologies currently employed in life sciences research, and discuss proteomic studies of uveal melanoma.

The analysis of predictability of α-decay half-life formulae and the α partial half-lives of some exotic nuclei

International Nuclear Information System (INIS)

Dasgupta-Schubert, N.; Reyes, M.A.; Tamez, V.A.

2009-01-01

The predictabilities of the three α-decay half-life formulae, the Royer GLDM, the Viola-Seaborg and the Sobiczewski-Parkhomenko formulae, have been evaluated by developing a method based on the ansatz of standard experimental benchmarking. The coefficients of each formula were re-derived using the reliable data of the α -standards nuclei. The modified formulae that resulted were used to evaluate the accuracies of the formulae towards the prediction of half-lives of a set of nuclides with well-studied α spectroscopic data as well as a set of exotic α emitters. Further, a simple linear optimisation of the modified formulae allowed adjustments for the insufficient statistics of the primary data set without changing the modified formulae. While the three modified formulae showed equivalent results for all the medium heavy nuclei except the odd-odd, the modified GLDM showed relatively the best figures of merit for the odd-odd and superheavy nuclides. (orig.)

Systematics of half-lives for proton radioactivity

International Nuclear Information System (INIS)

Medeiros, E.L.; Rodrigues, M.M.N.; Duarte, S.B.; Tavares, O.A.P.

2007-01-01

Half-life measurements for both ground-state and isomeric transitions in proton radioactivity are systematized by using a semiempirical, one-parameter model based on tunneling through a potential barrier, where the centrifugal and overlapping effects are taken into account within the spherical nucleus approximation. This approach, which has been successfully applied to alpha decay cases covering ∼ 30 orders of magnitude in half-life, has shown, in addition, very adequate at fitting all existing data on partial half-life, T 1/2p , of proton emission from nuclei. Nearly 70 measured half-life values have been analysed, and the data could be described by two straight lines relating the pure Coulomb contribution to half life with the quantity Z d (μ 0 /Q p ) 1/2 (Z d is the atomic number of the daughter nucleus, μ 0 is the reduced mass, and Q p is the total nuclear energy available for decay). These straight lines are shown to correspond to different degrees of deformation, namely, very prolate (δ> approx. 0.1), and other shaped (delta < approx. 0.1) parent nuclei. The goodness in reproducing the data attained in the present systematics allows for half-life predictions for a few possible cases of proton radioactivity not yet experimentally accessed. (author)

High-Precision Half-Life and Branching Ratio Measurements for the Superallowed β+ Emitter 26Alm

Science.gov (United States)

Finlay, P.; Svensson, C. E.; Demand, G. A.; Garrett, P. E.; Green, K. L.; Leach, K. G.; Phillips, A. A.; Rand, E. T.; Ball, G.; Bandyopadhyay, D.; Djongolov, M.; Ettenauer, S.; Hackman, G.; Pearson, C. J.; Leslie, J. R.; Andreoiu, C.; Cross, D.; Austin, R. A. E.; Grinyer, G. F.; Sumithrarachchi, C. S.; Williams, S. J.; Triambak, S.

2013-03-01

High-precision half-life and branching-ratio measurements for the superallowed β+ emitter 26Alm were performed at the TRIUMF-ISAC radioactive ion beam facility. An upper limit of ≤ 15 ppm at 90% C.L. was determined for the sum of all possible non-analogue β+/EC decay branches of 26Alm, yielding a superallowed branching ratio of 100.0000+0-0.0015%. A value of T1/2 = 6:34654(76) s was determined for the 26Alm half-life which is consistent with, but 2.5 times more precise than, the previous world average. Combining these results with world-average measurements yields an ft value of 3037.58(60) s, the most precisely determined for any superallowed emitting nucleus to date. This high-precision ft value for 26Alm provides a new benchmark to refine theoretical models of isospin-symmetry-breaking effects in superallowed β decays.

Subregion-Specific Proteomic Signature in the Hippocampus for Recognition Processes in Adult Mice

Directory of Open Access Journals (Sweden)

Lukas M. von Ziegler

2018-03-01

Full Text Available Summary: The hippocampal formation is a brain structure essential for higher-order cognitive functions. It has a complex anatomical organization and cellular composition, and hippocampal subregions have different properties and functional roles. In this study, we used SWATH-MS to determine whether the proteomes of hippocampus areas CA1 and CA3 can explain the commonalities or specificities of these subregions in basal conditions and after recognition memory. We show that the proteomes of areas CA1 and CA3 are largely different in basal conditions and that differential changes and dynamics in protein expression are induced in these areas after recognition of an object or object location. While changes are consistent across both recognition paradigms in area CA1, they are not in area CA3, suggesting distinct proteomic responses in areas CA1 and CA3 for memory formation. : How does the proteome differ in hippocampus areas CA1 and CA3? von Ziegler et al. identify the proteomes of areas CA1 and CA3 and characterize their dynamics during different recognition processes in adult mice. Keywords: hippocampus, areas CA1 and CA3, proteome, dynamics, object memory, object location memory, mass spectrometry, SWATH-MS, mice, bioinformatic tools

Proteomics methods applied to malaria: Plasmodium falciparum

International Nuclear Information System (INIS)

Cuesta Astroz, Yesid; Segura Latorre, Cesar

2012-01-01

Malaria is a parasitic disease that has a high impact on public health in developing countries. The sequencing of the plasmodium falciparum genome and the development of proteomics have enabled a breakthrough in understanding the biology of the parasite. Proteomics have allowed to characterize qualitatively and quantitatively the parasite s expression of proteins and has provided information on protein expression under conditions of stress induced by antimalarial. Given the complexity of their life cycle, this takes place in the vertebrate host and mosquito vector. It has proven difficult to characterize the protein expression during each stage throughout the infection process in order to determine the proteome that mediates several metabolic, physiological and energetic processes. Two dimensional electrophoresis, liquid chromatography and mass spectrometry have been useful to assess the effects of antimalarial on parasite protein expression and to characterize the proteomic profile of different p. falciparum stages and organelles. The purpose of this review is to present state of the art tools and advances in proteomics applied to the study of malaria, and to present different experimental strategies used to study the parasite's proteome in order to show the advantages and disadvantages of each one.

Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005.

Directory of Open Access Journals (Sweden)

Sabine Matallana-Surget

Full Text Available The filamentous cyanobacterium Arthrospira platensis has a long history of use as a food supply and it has been used by the European Space Agency in the MELiSSA project, an artificial microecosystem which supports life during long-term manned space missions. This study assesses progress in the field of cyanobacterial shotgun proteomics and light/dark diurnal cycles by focusing on Arthrospira platensis. Several fractionation workflows including gel-free and gel-based protein/peptide fractionation procedures were used and combined with LC-MS/MS analysis, enabling the overall identification of 1306 proteins, which represents 21% coverage of the theoretical proteome. A total of 30 proteins were found to be significantly differentially regulated under light/dark growth transition. Interestingly, most of the proteins showing differential abundance were related to photosynthesis, the Calvin cycle and translation processes. A novel aspect and major achievement of this work is the successful improvement of the cyanobacterial proteome coverage using a 3D LC-MS/MS approach, based on an immobilized metal affinity chromatography, a suitable tool that enabled us to eliminate the most abundant protein, the allophycocyanin. We also demonstrated that cell growth follows a light/dark cycle in A. platensis. This preliminary proteomic study has highlighted new characteristics of the Arthrospira platensis proteome in terms of diurnal regulation.

Real-World Analysis of Dispensed IUs of Coagulation Factor IX and Resultant Expenditures in Hemophilia B Patients Receiving Standard Half-life Versus Extended Half-life Products and Those Switching from Standard Half-life to Extended Half-life Products.

Science.gov (United States)

Tortella, Bartholomew J; Alvir, José; McDonald, Margaret; Spurden, Dean; Fogarty, Patrick F; Chhabra, Amit; Pleil, Andreas M

2018-01-24

Hemophilia B requires replacement therapy with factor IX (FIX) coagulation products to treat and prevent bleeding episodes. A recently introduced extended half-life (EHL) recombinant FIX replacement product provided the opportunity to compare the amount of dispensed factor and expenditures for EHL treatment compared with a standard half-life (SHL) product. To determine factor international units (IUs) dispensed and expenditures associated with switching from nonacog alfa, the most commonly used SHL replacement product, to eftrenonacog alfa, an EHL FIX replacement product. Two U.S. claims databases were analyzed. A large national specialty pharmacy dispensation claims database was used to identify the number of IUs dispensed and monthly charges for all patients with hemophilia B from April 2015 to June 2016. Truven Health MarketScan Research Databases (January 2010-July 2016) were used to identify IUs and expenditures for patients with claims data for at least 3 months before and after switching from the SHL to the EHL product. Medians for IUs and expenditures are presented to accommodate for skewness of data distribution. The national specialty pharmacy database analysis included 296 patients with moderate or severe hemophilia B (233 on SHL; 94 on EHL). Median monthly factor dispensed was 11% lower (2,142 IU) in the EHL versus SHL cohort over the study period, while individual monthly reductions ranged from 32% to 47% (9,838 IU to 16,514 IU). Using the wholesale acquisition cost, the median per-patient monthly factor expenditures over the 15-month study period were 94% higher ($23,005) for the EHL than for the SHL product. Individual median monthly expenditure differences ranged from 15% ($6,562) to 49% ($19,624). In the Truven database, 14 patients switched from the SHL to the EHL product. The amount of factor dispensed was variable; in the 1-year period before and after the switch from the SHL to the EHL product, mean IUs dispensed decreased by 3,005 IU, while

ORIGEN-S Decay Data Library and Half-Life Uncertainties

International Nuclear Information System (INIS)

Hermann, O.W.

1998-01-01

The results of an extensive update of the decay data of the ORIGEN-S library are presented in this report. The updated decay data were provided for both the ORIGEN-S and ORIGEN2 libraries in the same project. A complete edit of the decay data plus the available half-life uncertainties are included in Appendix A. A detailed description of the types of data contained in the library, the format of the library, and the data sources are also presented. Approximately 24% of the library nuclides are stable, 66% were updated from ENDF/B-VI, about 8% were updated from ENSDF, and the remaining 2% were not updated. Appendix B presents a listing of percentage changes in decay heat from the old to the updated library for all nuclides containing a difference exceeding 1% in any parameter

Half-life of the 3/2/sup +/ level of /sup 119/Sn

Energy Technology Data Exchange (ETDEWEB)

Abreu, M C; Gil, F B [Faculdade de Ciencias da Universidade de Lisboa, Lisbon (Portugal). Grupo de Espectroscopia Nuclear, Laboratorio de Fisica

1976-01-01

The half-life of the 3/2/sup +/, 23.87 keV level of /sup 119/Sn is measured by the delayed coincidence technique. Magnetic spectrometry associated with scintillation techniques and scintillation spectrometry only have been used. The results obtained with these techniques were respectively Tsub(1/2) = 17.87 +- 0.11 ns and Tsub(1/2) = 18.48 +- 0.30 ns. The measured reduced M1 transition probability is compared with the single-particle and Kisslinger and Sorensen model predictions.

Global dynamics of a nonlocal delayed reaction-diffusion equation on a half plane

Science.gov (United States)

Hu, Wenjie; Duan, Yueliang

2018-04-01

We consider a delayed reaction-diffusion equation with spatial nonlocality on a half plane that describes population dynamics of a two-stage species living in a semi-infinite environment. A Neumann boundary condition is imposed accounting for an isolated domain. To describe the global dynamics, we first establish some a priori estimate for nontrivial solutions after investigating asymptotic properties of the nonlocal delayed effect and the diffusion operator, which enables us to show the permanence of the equation with respect to the compact open topology. We then employ standard dynamical system arguments to establish the global attractivity of the nontrivial equilibrium. The main results are illustrated by the diffusive Nicholson's blowfly equation and the diffusive Mackey-Glass equation.

Pile-up corrections for high-precision superallowed β decay half-life measurements via γ-ray photopeak counting

Science.gov (United States)

Grinyer, G. F.; Svensson, C. E.; Andreoiu, C.; Andreyev, A. N.; Austin, R. A. E.; Ball, G. C.; Bandyopadhyay, D.; Chakrawarthy, R. S.; Finlay, P.; Garrett, P. E.; Hackman, G.; Hyland, B.; Kulp, W. D.; Leach, K. G.; Leslie, J. R.; Morton, A. C.; Pearson, C. J.; Phillips, A. A.; Sarazin, F.; Schumaker, M. A.; Smith, M. B.; Valiente-Dobón, J. J.; Waddington, J. C.; Williams, S. J.; Wong, J.; Wood, J. L.; Zganjar, E. F.

2007-09-01

A general technique that corrects γ-ray gated β decay-curve data for detector pulse pile-up is presented. The method includes corrections for non-zero time-resolution and energy-threshold effects in addition to a special treatment of saturating events due to cosmic rays. This technique is verified through a Monte Carlo simulation and experimental data using radioactive beams of Na26 implanted at the center of the 8π γ-ray spectrometer at the ISAC facility at TRIUMF in Vancouver, Canada. The β-decay half-life of Na26 obtained from counting 1809-keV γ-ray photopeaks emitted by the daughter Mg26 was determined to be T=1.07167±0.00055 s following a 27σ correction for detector pulse pile-up. This result is in excellent agreement with the result of a previous measurement that employed direct β counting and demonstrates the feasibility of high-precision β-decay half-life measurements through the use of high-purity germanium γ-ray detectors. The technique presented here, while motivated by superallowed-Fermi β decay studies, is general and can be used for all half-life determinations (e.g. α-, β-, X-ray, fission) in which a γ-ray photopeak is used to select the decays of a particular isotope.

Global dynamics of the Escherichia coli proteome and phosphoproteome during growth in minimal medium.

Science.gov (United States)

Soares, Nelson C; Spät, Philipp; Krug, Karsten; Macek, Boris

2013-06-07

Recent phosphoproteomics studies have generated relatively large data sets of bacterial proteins phosphorylated on serine, threonine, and tyrosine, implicating this type of phosphorylation in the regulation of vital processes of a bacterial cell; however, most phosphoproteomics studies in bacteria were so far qualitative. Here we applied stable isotope labeling by amino acids in cell culture (SILAC) to perform a quantitative analysis of proteome and phosphoproteome dynamics of Escherichia coli during five distinct phases of growth in the minimal medium. Combining two triple-SILAC experiments, we detected a total of 2118 proteins and quantified relative dynamics of 1984 proteins in all measured phases of growth, including 570 proteins associated with cell wall and membrane. In the phosphoproteomic experiment, we detected 150 Ser/Thr/Tyr phosphorylation events, of which 108 were localized to a specific amino acid residue and 76 were quantified in all phases of growth. Clustering analysis of SILAC ratios revealed distinct sets of coregulated proteins for each analyzed phase of growth and overrepresentation of membrane proteins in transition between exponential and stationary phases. The proteomics data indicated that proteins related to stress response typically associated with the stationary phase, including RpoS-dependent proteins, had increasing levels already during earlier phases of growth. Application of SILAC enabled us to measure median occupancies of phosphorylation sites, which were generally low (<12%). Interestingly, the phosphoproteome analysis showed a global increase of protein phosphorylation levels in the late stationary phase, pointing to a likely role of this modification in later phases of growth.

Biological half-life of bromide in the rat depends primarily on the magnitude of sodium intake

Czech Academy of Sciences Publication Activity Database

Pavelka, Stanislav; Babický, Arnošt; Vobecký, Miloslav

2005-01-01

Roč. 54, č. 6 (2005), s. 639-644 ISSN 0862-8408 Institutional research plan: CEZ:AV0Z50110509 Keywords : biological half-life * bromide * sodium Subject RIV: ED - Physiology Impact factor: 1.806, year: 2005

Fab-dsFv: A bispecific antibody format with extended serum half-life through albumin binding.

Science.gov (United States)

Davé, Emma; Adams, Ralph; Zaccheo, Oliver; Carrington, Bruce; Compson, Joanne E; Dugdale, Sarah; Airey, Michael; Malcolm, Sarah; Hailu, Hanna; Wild, Gavin; Turner, Alison; Heads, James; Sarkar, Kaushik; Ventom, Andrew; Marshall, Diane; Jairaj, Mark; Kopotsha, Tim; Christodoulou, Louis; Zamacona, Miren; Lawson, Alastair D; Heywood, Sam; Humphreys, David P

2016-10-01

An antibody format, termed Fab-dsFv, has been designed for clinical indications that require monovalent target binding in the absence of direct Fc receptor (FcR) binding while retaining substantial serum presence. The variable fragment (Fv) domain of a humanized albumin-binding antibody was fused to the C-termini of Fab constant domains, such that the VL and VH domains were individually connected to the Cκ and CH1 domains by peptide linkers, respectively. The anti-albumin Fv was selected for properties thought to be desirable to ensure a durable serum half-life mediated via FcRn. The Fv domain was further stabilized by an inter-domain disulfide bond. The bispecific format was shown to be thermodynamically and biophysically stable, and retained good affinity and efficacy to both antigens simultaneously. In in vivo studies, the serum half-life of Fab-dsFv, 2.6 d in mice and 7.9 d in cynomolgus monkeys, was equivalent to Fab'-PEG.

Unique proteomic signatures distinguish macrophages and dendritic cells.

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Lev Becker

Full Text Available Monocytes differentiate into heterogeneous populations of tissue macrophages and dendritic cells (DCs that regulate inflammation and immunity. Identifying specific populations of myeloid cells in vivo is problematic, however, because only a limited number of proteins have been used to assign cellular phenotype. Using mass spectrometry and bone marrow-derived cells, we provided a global view of the proteomes of M-CSF-derived macrophages, classically and alternatively activated macrophages, and GM-CSF-derived DCs. Remarkably, the expression levels of half the plasma membrane proteins differed significantly in the various populations of cells derived in vitro. Moreover, the membrane proteomes of macrophages and DCs were more distinct than those of classically and alternatively activated macrophages. Hierarchical cluster and dual statistical analyses demonstrated that each cell type exhibited a robust proteomic signature that was unique. To interrogate the phenotype of myeloid cells in vivo, we subjected elicited peritoneal macrophages harvested from wild-type and GM-CSF-deficient mice to mass spectrometric and functional analysis. Unexpectedly, we found that peritoneal macrophages exhibited many features of the DCs generated in vitro. These findings demonstrate that global analysis of the membrane proteome can help define immune cell phenotypes in vivo.

Thyroid fractional deposition and half life of radioiodine

International Nuclear Information System (INIS)

Fujita, Minoru

1974-01-01

In order to measure the absorbed dose of radioiodine in the thyroid gland, which was incorporated by halation or ingestion, iodine intake (fa), 131 I thyroid uptake rate(fw), 131 I thyroid uptake rate compared to the rate in the whole body (f 2 ) and the half life of iodine in the thyroid gland(Teff) were examined. Thyroid fractional deposition of 131 I was compared between Japanese and European. The rate of 131 I which moved from the blood into the thyroid gland in children (f 2 ') and the effect of the iodine in meals on 131 I thyroid uptake (fw) were also studied. In Japanese, f 2 was 0.28 and the mean Teff was 6.9 +- 0.7 days in 11 Japanese adults. There was an individual difference in these biological parameter and the values in adults were different from those in children. A little difference in value between Japanese and European suggested to be caused by the greater amount of stable iodine in meals in Japanese. (Serizawa, K.)

Influence of antithyroid medication on effective half-life and uptake of 131 I following radioiodine therapy

International Nuclear Information System (INIS)

Moka, D.; Voth, E.; Schicha, H.

1997-01-01

Aim: A radioiodine therapy (RIT) in thyrotoxic patients receiving antithyroid drugs (ATD) leads in comparison to nonpretreated patients either to higher therapeutic doses or to higher treatment failure rates. Aim of this study was to optimize the effect of RIT in patients pretreated with ATD. Methods: Therefore, the influence of ATD was assessed in 109 patients with shortened effective half-life of 131 I. RIT was performed under stationary conditions. Radioiodine activity of the thyroid gland was stopped three days after RIT. The patients antithyroid medication was stopped three days after RIT. The progress of the first RIT and of a second radioiodine application, which still was necessary in 29 patients, was compared to 32 patients receiving ATD, continuously. Results: Values of effective half-life for 131 I rose significantly from 3.2±0.2 to 5.7±0.2 days (Graves' disease: 3.4 to 5.7 days; toxic goiters' disease: Multifocal autonomy 3.2 to 6.2 days; unifocal autonomy 2.5 auf 5.0 days) 2-3 days after stopping ATD. There was an increase of the 131 I-uptake of a second RIT decreased significantly in patients receiving ATD, continuously. Conclusion: Effective half-life and uptake of 131 I was affected significantly by ATD. The stop taking of ATD after RIT is useful to improve an apparent insufficient RIT in thyrotoxic patients receiving ATD. (orig.) [de

Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications

Energy Technology Data Exchange (ETDEWEB)

Baker, Erin Shammel; Liu, Tao; Petyuk, Vladislav A.; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; Anderson, Gordon A.; Smith, Richard D.

2012-08-31

Mass spectrometry (MS)-based proteomics measurements have become increasingly utilized in a wide range of biological and biomedical applications, and have significantly enhanced the understanding of the complex and dynamic nature of the proteome and its connections to biology and diseases. While some MS techniques such as those for targeted analysis are increasingly applied with great success, others such as global quantitative analysis (for e.g. biomarker discovery) are more challenging and continue to be developed and refined to provide the desired throughput, sensitivity and/ or specificity. New MS capabilities and proteomics-based pipelines/strategies also keep enhancing for the advancement of clinical proteomics applications such as protein biomarker discovery and validation. Herein, we provide a brief review to summarize the current state of MS-based proteomics with respect to its advantages and present limitations, while highlighting its potential in future clinical applications.

Biomarker discovery in mass spectrometry-based urinary proteomics.

Science.gov (United States)

Thomas, Samuel; Hao, Ling; Ricke, William A; Li, Lingjun

2016-04-01

Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study on the biological half-life and organ-distribution of tritiated lysine-vasopressin in Brattleboro rats

International Nuclear Information System (INIS)

Laczi, F.; Laszlo, F.A.; Keri, Gy.; Teplan, I.

1980-01-01

The biological half-life and organ-distribution of tritiated lysine-vasopressin were determined in R-Amsterdam rats, and in homozygous and heterozygous Brattleboro rats with hereditary central diabetes insipidus. It was found that the biological half-life of the tritiated lysin-vasopressin in the Brattleboro rats did not differ significantly from that found in the R-Amsterdam rats. The highest radioactivities were observed in the neuro- and adenohypophyses and in the kidneys of both the R-Amsterdam and the Brattleboro rats. The accumulation of tritiated LVP was higher in the small intestine of the Brattleboro rats than in that of the R-Amsterdam animals. The results have led to the conclusion that the accelerated elimination of vasopressin and its pathologic organ-accumulation are probably not involved in the water metabolism disturbance of Brattleboro rats with hereditary hypothalamic diabetes insipidus. (author)

Fast renal trapping of porcine Luteinizing Hormone (pLH shown by 123I-scintigraphic imaging in rats explains its short circulatory half-life

Directory of Open Access Journals (Sweden)

Locatelli Alain

2003-10-01

Full Text Available Abstract Background Sugar moieties of gonadotropins play no primary role in receptor binding but they strongly affect their circulatory half-life and consequently their in vivo biopotencies. In order to relate more precisely hepatic trapping of these glycoproteic hormones with their circulatory half-life, we undertook a comparative study of the distribution and elimination of porcine LH (pLH and equine CG (eCG which exhibit respectively a short and a long half-life. This was done first by following half-lives of pLH in piglets with hepatic portal circulation shunted or not. It was expected that such a shunt would enhance the short half-life of pLH. Subsequently, scintigraphic imaging of both 123I-pLH and 123I-eCG was performed in intact rats to compare their routes and rates of distribution and elimination. Methods Native pLH or eCG was injected to normal piglets and pLH was tested in liver-shunted anæsthetized piglet. Blood samples were recovered sequentially over one hour time and the hormone concentrations were determined by a specific ELISA method. Scintigraphic imaging of 123I-pLH and 123I-eCG was performed in rats using a OPTI-CGR gamma camera. Results In liver-shunted piglets, the half-life of pLH was found to be as short as in intact piglets (5 min. In the rat, the half-life of pLH was also found to be very short (3–6 min and 123I-pLH was found to accumulate in high quantity in less than 10 min post injection at the level of kidneys but not in the liver. 123I-eCG didn't accumulate in any organ in the rats during the first hour, plasma concentrations of this gonadotropin being still elevated (80% at this time. Conclusion In both the porcine and rat species, the liver is not responsible for the rapid elimination of pLH from the circulation compared to eCG. Our scintigraphic experiments suggest that the very short circulatory half-life of LH is due to rapid renal trapping.

Maillard Proteomics: Opening New Pages

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Alena Soboleva

2017-12-01

Full Text Available Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer’s disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus, proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.

A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses.

Science.gov (United States)

Hall, Neil; Karras, Marianna; Raine, J Dale; Carlton, Jane M; Kooij, Taco W A; Berriman, Matthew; Florens, Laurence; Janssen, Christoph S; Pain, Arnab; Christophides, Georges K; James, Keith; Rutherford, Kim; Harris, Barbara; Harris, David; Churcher, Carol; Quail, Michael A; Ormond, Doug; Doggett, Jon; Trueman, Holly E; Mendoza, Jacqui; Bidwell, Shelby L; Rajandream, Marie-Adele; Carucci, Daniel J; Yates, John R; Kafatos, Fotis C; Janse, Chris J; Barrell, Bart; Turner, C Michael R; Waters, Andrew P; Sinden, Robert E

2005-01-07

Plasmodium berghei and Plasmodium chabaudi are widely used model malaria species. Comparison of their genomes, integrated with proteomic and microarray data, with the genomes of Plasmodium falciparum and Plasmodium yoelii revealed a conserved core of 4500 Plasmodium genes in the central regions of the 14 chromosomes and highlighted genes evolving rapidly because of stage-specific selective pressures. Four strategies for gene expression are apparent during the parasites' life cycle: (i) housekeeping; (ii) host-related; (iii) strategy-specific related to invasion, asexual replication, and sexual development; and (iv) stage-specific. We observed posttranscriptional gene silencing through translational repression of messenger RNA during sexual development, and a 47-base 3' untranslated region motif is implicated in this process.

Advancing cell biology through proteomics in space and time (PROSPECTS)

DEFF Research Database (Denmark)

Lamond, A.I.; Uhlen, M.; Horning, S.

2012-01-01

a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU......-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16...... quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how...

Proposal of a new model for dose calculation due to the inhalation of Ru-222, Ru-220 and their sons with brief half-life

International Nuclear Information System (INIS)

Mauricio, C.L.P.

1982-06-01

The consequences of the radiation interactions upon the human body are studied. In order to simulate by computer the radiation interaction of the atoms of radon and thoron atoms and their Sons with a brief half life inhaled with the cells, the compartimental dosimetric model is used. The metabolic pathway of those radionuclides is described by continuous medium dynamic differential equation. The energy transfer processes are seen in details. The individual retention function is determined by bio-analysis. The results of internal dosimetry are consistents with the new international recommendations from ICRP-32. (L.F.S.) [pt

Application of proteomics to ecology and population biology.

Science.gov (United States)

Karr, T L

2008-02-01

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System.

Science.gov (United States)

Farrelly, L A; Dill, B D; Molina, H; Birtwistle, M R; Maze, I

2016-01-01

Characterizing the dynamic behavior of nucleosomes in the central nervous system is vital to our understanding of brain-specific chromatin-templated processes and their roles in transcriptional plasticity. Histone turnover-the complete loss of old, and replacement by new, nucleosomal histones-is one such phenomenon that has recently been shown to be critical for cell-type-specific transcription in brain, synaptic plasticity, and cognition. Such revelations that histones, long believed to static proteins in postmitotic cells, are highly dynamic in neurons were only possible owing to significant advances in analytical chemistry-based techniques, which now provide a platform for investigations of histone dynamics in both healthy and diseased tissues. Here, we discuss both past and present proteomic methods (eg, mass spectrometry, human "bomb pulse labeling") for investigating histone turnover in brain with the hope that such information may stimulate future investigations of both adaptive and aberrant forms of "neuroepigenetic" plasticity. © 2016 Elsevier Inc. All rights reserved.

Absorption and biological half-life in humans of intrinsic and extrinsic 54Mn tracers from foods of plant origin

International Nuclear Information System (INIS)

Johnson, P.E.; Lykken, G.I.; Korynta, E.D.

1991-01-01

Absorption and biological half-life of 54 Mn were measured in adult men and women fed foods labeled intrinsically or extrinsically with 54 Mn. Each subject consumed a series of three test meals consisting of a food labeled intrinsically, a food labeled extrinsically or MnCl 2 (control) served in random order. The foods tested were lettuce, spinach, wheat and sunflower seeds. Lettuce meals and their controls contained 9.65 mumol Mn; other meals contained 22.50 mumol Mn. In addition to the test food or MnCl 2 , each meal consisted of vegetable oil (5 g), salt (NaCl, 0.15 g) and crackers (10 g), which provided 0.55 mumol Mn. There were no differences in percentage of Mn absorption or biological half-life of 54 Mn for any of the intrinsically/extrinsically labeled food pairs. Absorption of 54 Mn from MnCl 2 (8.90%) was greater than from lettuce (5.20%), spinach (3.81%), wheat (2.16%) or sunflower seeds (1.71%), but the biological half-life did not vary with the source of Mn. Absorption of 54 Mn from lettuce was significantly (P less than 0.05) greater than from wheat or sunflower seeds. Although the Mn dose in the test meal was less for lettuce than for the other foods, there was no difference in Mn absorption from MnCl 2 between the subjects fed lettuce and subjects fed other foods. There was no correlation of either 54 Mn absorption or biological half-life with whole blood or plasma Mn

The beta(+) decay and cosmic-ray half-life of Mn-54

Science.gov (United States)

Dacruz, M. T. F.; Norman, E. B.; Chan, Y. D.; Garcia, A.; Larimer, R. M.; Lesko, K. T.; Stokstad, R. G.; Wietfeldt, F. E.

1993-03-01

We performed a search for the beta(+) branch of Mn-54 decay. As a cosmic ray, Mn-54, deprived of its atomic electrons, can decay only via beta(+) and beta(-) decay, with a half-life of the order of 106 yr. This turns Mn-54 into a suitable cosmic chronometer for the study of cosmic-ray confinement times. We searched for coincident back-to-back 511-keV gamma-rays using two germanium detectors inside a Nal(Tl) annulus. An upper limit of 2 x 10-8 was found for the beta(+) decay branch, corresponding to a lower limit of 13.7 for the log ft value.

Asymmetric proteome equalization of the skeletal muscle proteome using a combinatorial hexapeptide library.

Directory of Open Access Journals (Sweden)

Jenny Rivers

Full Text Available Immobilized combinatorial peptide libraries have been advocated as a strategy for equalization of the dynamic range of a typical proteome. The technology has been applied predominantly to blood plasma and other biological fluids such as urine, but has not been used extensively to address the issue of dynamic range in tissue samples. Here, we have applied the combinatorial library approach to the equalization of a tissue where there is also a dramatic asymmetry in the range of abundances of proteins; namely, the soluble fraction of skeletal muscle. We have applied QconCAT and label-free methodology to the quantification of the proteins that bind to the beads as the loading is progressively increased. Although some equalization is achieved, and the most abundant proteins no longer dominate the proteome analysis, at high protein loadings a new asymmetry of protein expression is reached, consistent with the formation of complex assembles of heat shock proteins, cytoskeletal elements and other proteins on the beads. Loading at different ionic strength values leads to capture of different subpopulations of proteins, but does not completely eliminate the bias in protein accumulation. These assemblies may impair the broader utility of combinatorial library approaches to the equalization of tissue proteomes. However, the asymmetry in equalization is manifest at either low and high ionic strength values but manipulation of the solvent conditions may extend the capacity of the method.

From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform.

Science.gov (United States)

Weckwerth, Wolfram; Wienkoop, Stefanie; Hoehenwarter, Wolfgang; Egelhofer, Volker; Sun, Xiaoliang

2014-01-01

Genome sequencing and systems biology are revolutionizing life sciences. Proteomics emerged as a fundamental technique of this novel research area as it is the basis for gene function analysis and modeling of dynamic protein networks. Here a complete proteomics platform suited for functional genomics and systems biology is presented. The strategy includes MAPA (mass accuracy precursor alignment; http://www.univie.ac.at/mosys/software.html ) as a rapid exploratory analysis step; MASS WESTERN for targeted proteomics; COVAIN ( http://www.univie.ac.at/mosys/software.html ) for multivariate statistical analysis, data integration, and data mining; and PROMEX ( http://www.univie.ac.at/mosys/databases.html ) as a database module for proteogenomics and proteotypic peptides for targeted analysis. Moreover, the presented platform can also be utilized to integrate metabolomics and transcriptomics data for the analysis of metabolite-protein-transcript correlations and time course analysis using COVAIN. Examples for the integration of MAPA and MASS WESTERN data, proteogenomic and metabolic modeling approaches for functional genomics, phosphoproteomics by integration of MOAC (metal-oxide affinity chromatography) with MAPA, and the integration of metabolomics, transcriptomics, proteomics, and physiological data using this platform are presented. All software and step-by-step tutorials for data processing and data mining can be downloaded from http://www.univie.ac.at/mosys/software.html.

Energy dependence of average half-life of delayed neutron precursors in fast neutron induced fission of 235U and 236U

International Nuclear Information System (INIS)

Isaev, S.G.; Piksaikin, L.E.; Kazakov, L.E.; Tarasko, M.Z.

2000-01-01

The measurements of relative abundances and periods of delayed neutrons from fast neutron induced fission of 235 U and 236 U have been made at the electrostatic accelerator CG-2.5 at IPPE. The preliminary results were obtained and discussed in the frame of the systematics of the average half-life of delayed neutron precursors. It was shown that the average half-life value in both reactions depends on the energy of primary neutrons [ru

Measurement of the two-neutrino double-beta decay half-life of {sup 130}Te with the CUORE-0 experiment

Energy Technology Data Exchange (ETDEWEB)

Alduino, C.; Avignone, F.T.; Chott, N.; Creswick, R.J.; Rosenfeld, C.; Wilson, J. [University of South Carolina, Department of Physics and Astronomy, Columbia, SC (United States); Alfonso, K.; Hickerson, K.P.; Huang, H.Z.; Liu, X.; Trentalange, S.; Zhu, B.X. [University of California, Department of Physics and Astronomy, Los Angeles, CA (United States); Artusa, D.R. [University of South Carolina, Department of Physics and Astronomy, Columbia, SC (United States); INFN-Laboratori Nazionali del Gran Sasso, Assergi, L' Aquila (Italy); Azzolini, O.; Camacho, A.; Keppel, G.; Palmieri, V.; Pira, C. [INFN-Laboratori Nazionali di Legnaro, Legnaro, Padova (Italy); Banks, T.I.; Drobizhev, A.; Freedman, S.J.; Hennings-Yeomans, R.; O' Donnell, T.; Wagaarachchi, S.L. [University of California, Department of Physics, Berkeley, CA (United States); Lawrence Berkeley National Laboratory, Nuclear Science Division, Berkeley, CA (United States); Bari, G.; Deninno, M.M. [INFN-Sezione di Bologna, Bologna (Italy); Beeman, J.W. [Lawrence Berkeley National Laboratory, Materials Science Division, Berkeley, CA (United States); Bellini, F.; Cardani, L.; Casali, N.; Cosmelli, C.; Ferroni, F. [Sapienza Universita di Roma, Dipartimento di Fisica, Rome (Italy); INFN-Sezione di Roma, Rome (Italy); Bersani, A.; Caminata, A. [INFN-Sezione di Genova, Genova (Italy); Biassoni, M.; Carbone, L.; Cremonesi, O.; Ferri, E.; Giachero, A.; Pessina, G.; Previtali, E.; Rusconi, C. [INFN-Sezione di Milano Bicocca, Milan (Italy); Brofferio, C.; Capelli, S.; Carniti, P.; Cassina, L.; Chiesa, D.; Clemenza, M.; Faverzani, M.; Fiorini, E.; Gironi, L.; Gotti, C.; Maino, M.; Nucciotti, A.; Pavan, M.; Pozzi, S.; Sisti, M.; Terranova, F.; Zanotti, L. [Universita di Milano-Bicocca, Dipartimento di Fisica, Milan (Italy); INFN-Sezione di Milano Bicocca, Milan (Italy); Bucci, C.; Cappelli, L.; D' Addabbo, A.; Di Vacri, M.L.; Gorla, P.; Pattavina, L.; Pirro, S. [INFN-Laboratori Nazionali del Gran Sasso, Assergi, L' Aquila (Italy); Canonica, L. [INFN-Laboratori Nazionali del Gran Sasso, Assergi, L' Aquila (Italy); Massachusetts Institute of Technology, Cambridge, MA (United States); Cao, X.G.; Fang, D.Q.; Ma, Y.G.; Wang, H.W.; Zhang, G.Q. [Chinese Academy of Sciences, Shanghai Institute of Applied Physics, Shanghai (China); Copello, S.; Di Domizio, S.; Fernandes, G.; Marini, L.; Pallavicini, M. [INFN-Sezione di Genova, Genova (Italy); Universita di Genova, Dipartimento di Fisica, Genova (Italy); Cushman, J.S.; Davis, C.J.; Heeger, K.M.; Lim, K.E.; Maruyama, R.H. [Yale University, Department of Physics, New Haven, CT (United States); Dafinei, I.; Morganti, S.; Mosteiro, P.J.; Orio, F.; Pettinacci, V.; Tomei, C.; Vignati, M. [INFN-Sezione di Roma, Rome (Italy); Dell' Oro, S. [INFN-Laboratori Nazionali del Gran Sasso, Assergi, L' Aquila (Italy); INFN-Gran Sasso Science Institute, L' Aquila (Italy); Feintzeig, J.; Fujikawa, B.K.; Mei, Y.; Smith, A.R. [Lawrence Berkeley National Laboratory, Nuclear Science Division, Berkeley, CA (United States); Franceschi, M.A.; Ligi, C.; Napolitano, T.; Piperno, G. [INFN-Laboratori Nazionali di Frascati, Frascati, Rome (Italy); Giuliani, A.; Tenconi, M. [Universite Paris-Saclay, CSNSM, Univ. Paris-Sud, CNRS/IN2P3, Orsay (France); Gladstone, L.; Leder, A.; Winslow, L.A. [Massachusetts Institute of Technology, Cambridge, MA (United States); Gutierrez, T.D. [California Polytechnic State University, Physics Department, San Luis Obispo, CA (United States); Haller, E.E. [Lawrence Berkeley National Laboratory, Materials Science Division, Berkeley, CA (United States); University of California, Department of Materials Science and Engineering, Berkeley, CA (United States); Han, K. [Yale University, Department of Physics, New Haven, CT (United States); Shanghai Jiao Tong University, Department of Physics and Astronomy, Shanghai (China); Hansen, E. [University of California, Department of Physics and Astronomy, Los Angeles, CA (United States); Massachusetts Institute of Technology, Cambridge, MA (United States); Kadel, R. [Lawrence Berkeley National Laboratory, Physics Division, Berkeley, CA (United States); Kolomensky, Yu.G. [University of California, Department of Physics, Berkeley, CA (United States); Lawrence Berkeley National Laboratory, Nuclear Science Division, Berkeley, CA (United States); Lawrence Berkeley National Laboratory, Physics Division, Berkeley, CA (United States); Martinez, M. [Sapienza Universita di Roma, Dipartimento di Fisica, Rome (Italy); INFN-Sezione di Roma, Rome (Italy); Universidad de Zaragoza, Laboratorio de Fisica Nuclear y Astroparticulas, Zaragoza (Spain); Moggi, N. [INFN-Sezione di Bologna, Bologna (Italy); Alma Mater Studiorum-Universita di Bologna, Dipartimento di Scienze per la Qualita della Vita, Bologna (Italy); Nones, C. [Service de Physique des Particules, CEA/Saclay, Gif-sur-Yvette (France); Norman, E.B.; Wang, B.S. [Lawrence Livermore National Laboratory, Livermore, CA (United States); University of California, Department of Nuclear Engineering, Berkeley, CA (United States); Ouellet, J.L. [University of California, Department of Physics, Berkeley, CA (United States); Lawrence Berkeley National Laboratory, Nuclear Science Division, Berkeley, CA (United States); Massachusetts Institute of Technology, Cambridge, MA (United States); Pagliarone, C.E. [INFN-Laboratori Nazionali del Gran Sasso, Assergi, L' Aquila (Italy); Universita degli Studi di Cassino e del Lazio Meridionale, Dipartimento di Ingegneria Civile e Meccanica, Cassino (Italy); Sangiorgio, S.; Scielzo, N.D. [Lawrence Livermore National Laboratory, Livermore, CA (United States); Santone, D. [INFN-Laboratori Nazionali del Gran Sasso, Assergi, L' Aquila (Italy); Universita dell' Aquila, Dipartimento di Scienze Fisiche e Chimiche, L' Aquila (Italy); Singh, V. [University of California, Department of Physics, Berkeley, CA (US); Taffarello, L. [INFN-Sezione di Padova, Padova (IT); Wise, T. [Yale University, Department of Physics, New Haven, CT (US); University of Wisconsin, Department of Physics, Madison, WI (US); Woodcraft, A. [University of Edinburgh, SUPA, Institute for Astronomy, Edinburgh (GB); Zimmermann, S. [Lawrence Berkeley National Laboratory, Engineering Division, Berkeley, CA (US); Zucchelli, S. [INFN-Sezione di Bologna, Bologna (IT); Alma Mater Studiorum-Universita di Bologna, Dipartimento di Fisica e Astronomia, Bologna (IT)

2017-01-15

We report on the measurement of the two-neutrino double-beta decay half-life of {sup 130}Te with the CUORE-0 detector. From an exposure of 33.4 kg year of TeO{sub 2}, the half-life is determined to be T{sub 1/2}{sup 2ν} = [8.2 ± 0.2 (stat.) ± 0.6 (syst.)] x 10{sup 20} year. This result is obtained after a detailed reconstruction of the sources responsible for the CUORE-0 counting rate, with a specific study of those contributing to the {sup 130}Te neutrinoless double-beta decay region of interest. (orig.)

Dynamic heterogeneity and life history variability in the kittiwake

DEFF Research Database (Denmark)

Steiner, Uli; Tuljapurkar, Shripad; Orzack, Steven Hecht

2010-01-01

1. Understanding the evolution of life histories requires an assessment of the process that generates variation in life histories. Within-population heterogeneity of life histories can be dynamically generated by stochastic variation of reproduction and survival or be generated by individual...... differences that are fixed at birth. 2. We show for the kittiwake that dynamic heterogeneity is a sufficient explanation of observed variation of life histories. 3. The total heterogeneity in life histories has a small contribution from reproductive stage dynamics and a large contribution from survival...... differences. We quantify the diversity in life histories by metrics computed from the generating stochastic process. 4. We show how dynamic heterogeneity can be used as a null model and also how it can lead to positive associations between reproduction and survival across the life span. 5. We believe our...

Measurement of the two neutrino double beta decay half-life of Zr-96 with the NEMO-3 detector

Energy Technology Data Exchange (ETDEWEB)

Argyriades, J. [LAL, Universite Paris-Sud 11, CNRS/IN2P3, F-91405 Orsay (France); Arnold, R. [IPHC, Universite de Strasbourg, CNRS/IN2P3, F-67037 Strasbourg (France); Augier, C. [LAL, Universite Paris-Sud 11, CNRS/IN2P3, F-91405 Orsay (France); Baker, J. [INL, Idaho National Laboratory, 83415 Idaho Falls (United States); Barabash, A.S. [ITEP, Institute of Theoretical and Experimental Physics, 117259 Moscow (Russian Federation); Basharina-Freshville, A. [University College London, WC1E 6BT London (United Kingdom); Bongrand, M. [LAL, Universite Paris-Sud 11, CNRS/IN2P3, F-91405 Orsay (France); Broudin-Bay, G. [Universite Bordeaux, CENBG, UMR 5797, F-33175 Gradignan (France); CNRS/IN2P3, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France); Brudanin, V. [JINR, Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Caffrey, A.J. [INL, Idaho National Laboratory, 83415 Idaho Falls (United States); Chapon, A. [LPC, ENSICAEN, Universite de Caen, CNRS/IN2P3, F-14032 Caen (France); Chauveau, E. [Universite Bordeaux, CENBG, UMR 5797, F-33175 Gradignan (France); CNRS/IN2P3, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France); Daraktchieva, Z. [University College London, WC1E 6BT London (United Kingdom); Durand, D. [LPC, ENSICAEN, Universite de Caen, CNRS/IN2P3, F-14032 Caen (France); Egorov, V. [JINR, Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation); Fatemi-Ghomi, N. [University of Manchester, M13 9PL Manchester (United Kingdom); Flack, R. [University College London, WC1E 6BT London (United Kingdom); Guillon, B. [LPC, ENSICAEN, Universite de Caen, CNRS/IN2P3, F-14032 Caen (France); Hubert, Ph. [Universite Bordeaux, CENBG, UMR 5797, F-33175 Gradignan (France); CNRS/IN2P3, Centre d' Etudes Nucleaires de Bordeaux Gradignan, UMR5797, F-33175 Gradignan (France); Jullian, S. [LAL, Universite Paris-Sud 11, CNRS/IN2P3, F-91405 Orsay (France)

2010-12-08

Using 9.4 g of {sup 96}Zr isotope and 1221 days of data from the NEMO-3 detector corresponding to 0.031 kg y, the obtained 2{nu}{beta}{beta} decay half-life measurement is T{sub 1/2}{sup 2{nu}=}[2.35{+-}0.14(stat){+-}0.16(syst)]x10{sup 19} yr. Different characteristics of the final state electrons have been studied, such as the energy sum, individual electron energy, and angular distribution. The 2{nu} nuclear matrix element is extracted using the measured 2{nu}{beta}{beta} half-life and is M{sup 2{nu}=}0.049{+-}0.002. Constraints on 0{nu}{beta}{beta} decay have also been set.

Biological half-life of radiophosphorus in desert locust, Schistocerca gregaria Forskal (orthoptera:acrididae)

International Nuclear Information System (INIS)

Ulagaraj, S.M.; Singh, K.M.; Sethi, G.R.

1975-01-01

Adult desert locust, Schistocerca gregaria Forskal were fed with cabbage leaves, painted with carrier free 32 P 1mCi/ml. Radioactivity of five adults of both sexes and of feces was measured daily for 28 days. The amount of radioactivity appearing in the feces of males was consistently below that found in female locusts. The mean biological half-life of 32 P for males and females were 35.04 and 15.01 days, respectively. (author)

Advances in therapeutic Fc engineering - modulation of IgG associated effector functions and serum half-life

Directory of Open Access Journals (Sweden)

Abhishek Saxena

2016-12-01

Full Text Available Today monoclonal immunoglobulin gamma (IgG antibodies have become a major option in cancer therapy especially for the patients with advanced or metastatic cancers. Efficacy of monoclonal antibodies (mAbs are achieved through both its antigen binding fragment (Fab and crystallizable fragment (Fc. Fab can specifically recognize tumor associated antigen (TAA and thus modulate TAA-linked downstream signaling pathways that may lead to inhibition of tumor growth, induction of tumor apoptosis and differentiation. The Fc region can further improve mAbs’ efficacy by mediating effector functions such as antibody-dependent cellular cytotoxicity (ADCC, complement-dependent cytotoxicity (CDC and antibody dependent cell-mediated phagocytosis (ADCP. Moreover, Fc is the region interacting with the neonatal Fc receptor (FcRn in a pH-dependent manner that can slow down IgG’s degradation and extend its serum half-life. Loss of the antibody Fc region dramatically shortens its serum half-life and weakens its anti-cancer effects. Given the essential roles that the Fc region plays in the modulation of the efficacy of mAb in cancer treatment, Fc engineering has been extensively studied in the past years. This review focuses on the recent advances in therapeutic Fc engineering that modulates its related effector functions and serum half-life. We also discuss the progress made in aglycosylated mAb development that may substantially reduce cost of manufacture but maintain similar efficacies as conventional glycosylated mAb. Finally, we highlight several Fc engineering based mAbs under clinical trials.

Alteration of protein levels during influenza virus H1N1 infection in host cells: a proteomic survey of host and virus reveals differential dynamics.

Directory of Open Access Journals (Sweden)

Susann Kummer

Full Text Available We studied the dynamics of the proteome of influenza virus A/PR/8/34 (H1N1 infected Madin-Darby canine kidney cells up to 12 hours post infection by mass spectrometry based quantitative proteomics using the approach of stable isotope labeling by amino acids in cell culture (SILAC. We identified 1311 cell proteins and, apart from the proton channel M2, all major virus proteins. Based on their abundance two groups of virus proteins could be distinguished being in line with the function of the proteins in genesis and formation of new virions. Further, the data indicate a correlation between the amount of proteins synthesized and their previously determined copy number inside the viral particle. We employed bioinformatic approaches such as functional clustering, gene ontology, and pathway (KEGG enrichment tests to uncover co-regulated cellular protein sets, assigned the individual subsets to their biological function, and determined their interrelation within the progression of viral infection. For the first time we are able to describe dynamic changes of the cellular and, of note, the viral proteome in a time dependent manner simultaneously. Through cluster analysis, time dependent patterns of protein abundances revealed highly dynamic up- and/or down-regulation processes. Taken together our study provides strong evidence that virus infection has a major impact on the cell status at the protein level.

A new value for the half-life of {sup 10}Be by Heavy-Ion Elastic Recoil Detection and liquid scintillation counting

Energy Technology Data Exchange (ETDEWEB)

Korschinek, G., E-mail: Gunther.Korschinek@ph.tum.d [Physik Department, Technische Universitaet Muenchen, D-85748 Garching (Germany); Bergmaier, A. [Universitaet der Bundeswehr Muenchen, Fakultaet fuer Luft- und Raumfahrttechnik, Institut fuer Angewandte Physik und Messtechnik LRT2, Werner-Heisenberg-Weg 39, D-85577 Neubiberg (Germany); Faestermann, T. [Physik Department, Technische Universitaet Muenchen, D-85748 Garching (Germany); Gerstmann, U.C. [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Radiation Protection, Ingolstaedter Landstr. 1, D-85764 Neuherberg (Germany); Knie, K.; Rugel, G. [Physik Department, Technische Universitaet Muenchen, D-85748 Garching (Germany); Wallner, A. [VERA Laboratory, Faculty of Physics, University of Vienna, Waehringer Strasse 17, A-1090 Wien (Austria); Dillmann, I. [Physik Department, Technische Universitaet Muenchen, D-85748 Garching (Germany); Dollinger, G. [Universitaet der Bundeswehr Muenchen, Fakultaet fuer Luft- und Raumfahrttechnik, Institut fuer Angewandte Physik und Messtechnik LRT2, Werner-Heisenberg-Weg 39, D-85577 Neubiberg (Germany); Lierse von Gostomski, Ch. [Lehrstuhl fuer Radiochemie, Technische Universitaet Muenchen, D-85748 Garching (Germany); Kossert, K. [Physikalisch-Technische Bundesanstalt, Braunschweig (Germany); Maiti, M.; Poutivtsev, M. [Physik Department, Technische Universitaet Muenchen, D-85748 Garching (Germany); Remmert, A. [Lehrstuhl fuer Radiochemie, Technische Universitaet Muenchen, D-85748 Garching (Germany)

2010-01-15

The importance of {sup 10}Be in different applications of accelerator mass spectrometry (AMS) is well-known. In this context the half-life of {sup 10}Be has a crucial impact, and an accurate and precise determination of the half-life is a prerequisite for many of the applications of {sup 10}Be in cosmic-ray and earth science research. Recently, the value of the {sup 10}Be half-life has been the centre of much debate. In order to overcome uncertainties inherent in previous determinations, we introduced a new method of high accuracy and precision. An aliquot of our highly enriched {sup 10}Be master solution was serially diluted with increasing well-known masses of {sup 9}Be. We then determined the initial {sup 10}Be concentration by least square fit to the series of measurements of the resultant {sup 10}Be/{sup 9}Be ratio. In order to minimize uncertainties because of mass bias which plague other low-energy mass spectrometric methods, we used for the first time Heavy-Ion Elastic Recoil Detection (HI-ERD) for the determination of the {sup 10}Be/{sup 9}Be isotopic ratios, a technique which does not suffer from difficult to control mass fractionation. The specific activity of the master solution was measured by means of accurate liquid scintillation counting (LSC). The resultant combination of the {sup 10}Be concentration and activity yields a {sup 10}Be half-life of T{sub 1/2} = 1.388 +- 0.018 (1 s, 1.30%) Ma. In a parallel but independent study (Chmeleff et al. ), found a value of 1.386 +- 0.016 (1.15%) Ma. Our recommended weighted mean and mean standard error for the new value for {sup 10}Be half-life based on these two independent measurements is 1.387 +- 0.012 (0.87%) Ma.

Time, space, and disorder in the expanding proteome universe.

Science.gov (United States)

Minde, David-Paul; Dunker, A Keith; Lilley, Kathryn S

2017-04-01

Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins' dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms. © 2017 The Authors. Proteomics Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vitamin E plasma kinetics in swine show low bioavailability and short half-life of -α-tocopheryl acetate.

Science.gov (United States)

van Kempen, T A T G; Reijersen, M H; de Bruijn, C; De Smet, S; Michiels, J; Traber, M G; Lauridsen, C

2016-10-01

Vitamin E is important for animal production because of its effects on health and product quality, but the amount and form required remains controversial. Our objective was to quantify the absolute bioavailability of oral -α-tocopheryl acetate (α-TAc) in swine (22 ± 1 kg and 8 wk old, fitted with jugular catheters) adapted to a diet supplemented with 75 mg/kg -α-TAc; 75 mg/kg was chosen because this level represents the nonweighted average inclusion level in piglet diets across Western key swine-producing countries. For this, a 350-g test meal (6% fat) was supplied at time 0 containing 75 mg deuterated (D9) -α-TAc to 9 animals, and 8 animals received an intravenous () dose containing deuterated (D6) RRR-α-tocopherol (α-T) at one-eighth the oral dose and a test meal without supplemental vitamin E. Plasma samples (12 to 13 per animal) were obtained at incremental intervals over 75 h for analysis of deuterated α-T using liquid chromatography-tandem mass spectrometry. Surprisingly, the i.v. dose rapidly disappeared from plasma and then reappeared. The half-life for this first peak was only 1.7 ± 0.3 min. The second peak had an appearance rate (Ka) of 0.10 ± 0.06 d and a half-life of 5.9 ± 1.2 h. Oral dosing resulted, after a lag of 56 min, in a Ka of 0.91 ± 0.21 d and a half-life of 2.6 ± 0.8 h. The bioavailability for oral α-TAc was 12.5%, whereas the area under the curve was only 5.4%. This low bioavailability, small area under the curve, and short half-life are likely because of various factors, that is, the use of only 6% fat in the diet, the use of the acetate ester and , and the high dose relative to requirements. In conclusion, i.v. dosed vitamin E shows both a rapid and a very slow pool, whereas orally dosed vitamin E shows a single slow pool. The oral material has a very short half-live (44% of i.v. or 2.6 h), low bioavailability (12.5%), and a very small area under the curve (5.4%), bringing into question the efficacy of typical doses of vitamin

Measurement of the half-life of sup 1 sup 7 sup 6 Lu

CERN Document Server

Nir-El, Y

1998-01-01

The half-life of sup 1 sup 7 sup 6 Lu was determined by measuring the disintegration rate of a solution of lutetium oxide, using a calibrated HPGe detector, and found to be (3.69+-0.02)x10 sup 1 sup 0 y. It is recommended that the current adopted value be calculated from the grouping of three published values since 1983, including our value, the weighted mean of which is (3.73+-0.01)x10 sup 1 sup 0 y.

Biological half-life of iodine in adults with intact thyroid function and in athyreotic persons

Energy Technology Data Exchange (ETDEWEB)

Kramer, G.H.; Hauck, B.M.; Chamberlain, M.J

2002-07-01

A joint project between the Human Monitoring Laboratory (HML) and the Ottawa Hospital has measured the retention of {sup 131}I in patients who have received the radioiodine diagnostically. Thirty-nine subjects with intact thyroid glands and nine athyreotic subjects were measured in the HML's whole-body/thyroid counter to determine the retention of {sup 131}I following its medical administration. The average biological half-life of {sup 131}I in 26 euthyroid subjects was found to be 66.1{+-}6.3 days which may be statistically significantly lower than the ICRP recommended value of 80 days. Nine hyperthyroid patients had a mean biological half-life of 38.2{+-}8.6 days and in three hypothyroid patients the corresponding value was 29.3{+-}8.8 days. Thyroid {sup 131}I uptake was measured in a conventional clinical fashion at the Ottawa Hospital Civic campus 24 h after oral administration of the radioiodine using a collimated thick sodium iodide detector placed over the neck arteriorly. Measured values were 0.144{+-}0.009, 0.314{+-}0.035 and 0.045{+-}0.010 of the administered dose in euthyroid, hyperthyroid and hypothyroid patients respectively. The euthyroid range at the hospital is 0.06-0.22. Uptake was significantly lower for the euthyroid group than the ICRP value of 0.3. The radioiodine retention in athyreotic subjects followed a two compartment model with biological half-lives of 1.0{+-}0.2 days and 18.4{+-}1.1. days. (author)

Analytical studies by activation. Part A and B: Counting of short half-life radio-nuclides. Part C: Analytical programs for decay curves

International Nuclear Information System (INIS)

Junod, E.

1966-03-01

Part A and B: Since a radio-nuclide of short half-life is characterized essentially by the decrease in its activity even while it is being measured, the report begins by recalling the basic relationships linking the half-life the counting time, the counting rate and the number of particles recorded. The second part is devoted to the problem of corrections for counting losses due to the idle period of multichannel analyzers. Exact correction formulae have been drawn up for the case where the short half-life radionuclide is pure or contains only a long half-life radio-nuclide. By comparison, charts have been drawn up showing the approximations given by the so-called 'active time' counting and by the counting involving the real time associated with a measurement of the overall idle period, this latter method proving to be more valid than the former. A method is given for reducing the case of a complex mixture to that of a two-component mixture. Part C: The problems connected with the qualitative and quantitative analysis of the decay curves of a mixture of radioactive sources of which one at least has a short half-life are presented. A mathematical description is given of six basic processes for which some elements of Fortran programs are proposed. Two supplementary programs are drawn up for giving an overall treatment of problems of dosage in activation analysis: one on the basis of a simultaneous irradiation of the sample and of one or several known samples, the other with separate irradiation of the unknown and known samples, a dosimeter (activation, or external) being used for normalizing the irradiation flux conditions. (author) [fr

Trypanosoma cruzi alkaline 2-DE: Optimization and application to comparative proteome analysis of flagellate life stages

Directory of Open Access Journals (Sweden)

Santana Jaime M

2008-09-01

Full Text Available Abstract Background Trypanosoma cruzi, a flagellate protozoan, is the etiological agent of Chagas disease, a chronic illness that causes irreversible damage to heart and digestive tract in humans. Previous 2-DE analyses of T. cruzi proteome have not focused on basic proteins, possibly because of inherent difficulties for optimizing 2-DE in the alkaline pH range. However, T. cruzi wide pH range 2-DE gels have shown few visible spots in the alkaline region, indicating that the parasite either did not have an appreciable amount of alkaline proteins or that these proteins were underrepresented in the 2-DE gels. Results Different IEF conditions using 6–11 pH gradient strips were tested for separation of T. cruzi alkaline proteins. The optimized methodology described here was performed using anodic "paper bridge" sample loading supplemented by increased concentration of DTT and Triton X-100 on Multiphor II (GE Healthcare equipment and an electrode pad embedded in DTT- containing solution near the cathode in order to avoid depletion of reducing agent during IEF. Landmark proteins were identified by peptide mass fingerprinting allowing the production of an epimastigote 2-DE map. Most identified proteins corresponded to metabolic enzymes, especially those related to amino acid metabolism. The optimized 2-DE protocol was applied in combination with the "two-in-one gel" method to verify the relative expression of the identified proteins between samples from epimastigote and trypomastigote life stages. Conclusion High resolution 2-DE gels of T. cruzi life forms were achieved using the optimized methodology and a partial epimastigote alkaline 2-DE map was built. Among 700 protein spots detected, 422 were alkaline with a pI above 7.0. The "two-in-one gel" method simplified the comparative analysis between T. cruzi life stages since it minimized variations in spot migration and silver-stained spot volumes. The comparative data were in agreement with

Clinical proteomics: Current status, challenges, and future perspectives

Directory of Open Access Journals (Sweden)

Shyh-Horng Chiou

2011-01-01

Full Text Available This account will give an overview and evaluation of the current advances in mass spectrometry (MS-based proteomics platforms and technology. A general review of some background information concerning the application of these methods in the characterization of molecular sizes and related protein expression profiles associated with different types of cells under varied experimental conditions will be presented. It is intended to provide a concise and succinct overview to those clinical researchers first exposed to this foremost powerful methodology in modern life sciences of postgenomic era. Proteomic characterization using highly sophisticated and expensive instrumentation of MS has been used to characterize biological samples of complex protein mixtures with vastly different protein structure and composition. These systems are then used to highlight the versatility and potential of the MS-based proteomic strategies for facilitating protein expression analysis of various disease-related organisms or tissues of interest. Major MS-based strategies reviewed herein include (1 matrix-assisted laser desorption ionization-MS and electron-spray ionization proteomics; (2 one-dimensional or two-dimensional gel-based proteomics; (3 gel-free shotgun proteomics in conjunction with liquid chromatography/tandem MS; (4 Multiple reaction monitoring coupled tandem MS quantitative proteomics and; (5 Phosphoproteomics based on immobilized metal affinity chromatography and liquid chromatography-MS/MS.

Proteome-wide dataset supporting functional study of tyrosine kinases in breast cancer

Directory of Open Access Journals (Sweden)

Nicos Angelopoulos

2016-06-01

Full Text Available Tyrosine kinases (TKs play an essential role in regulating various cellular activities and dysregulation of TK signaling contributes to oncogenesis. However, less than half of the TKs have been thoroughly studied. Through a combined use of RNAi and stable isotope labeling with amino acids in cell culture (SILAC-based quantitative proteomics, a global functional proteomic landscape of TKs in breast cancer was recently revealed highlighting a comprehensive and highly integrated signaling network regulated by TKs (Stebbing et al., 2015 [1]. We collate the enormous amount of the proteomic data in an open access platform, providing a valuable resource for studying the function of TKs in cancer and benefiting the science community. Here we present a detailed description related to this study (Stebbing et al., 2015 [1] and the raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002065.

Estimating the biological half-life for radionuclides in homoeothermic vertebrates: a simplified allometric approach

Energy Technology Data Exchange (ETDEWEB)

Beresford, N.A. [Lancaster Environment Centre, NERC Centre for Ecology and Hydrology, Lancaster (United Kingdom); Vives i Batlle, J. [Belgian Nuclear Research Centre, Mol (Belgium)

2013-11-15

The application of allometric, or mass-dependent, relationships within radioecology has increased with the evolution of models to predict the exposure of organisms other than man. Allometry presents a method of addressing the lack of empirical data on radionuclide transfer and metabolism for the many radionuclide-species combinations which may need to be considered. However, sufficient data across a range of species with different masses are required to establish allometric relationships and this is not always available. Here, an alternative allometric approach to predict the biological half-life of radionuclides in homoeothermic vertebrates which does not require such data is derived. Biological half-life values are predicted for four radionuclides and compared to available data for a range of species. All predictions were within a factor of five of the observed values when the model was parameterised appropriate to the feeding strategy of each species. This is an encouraging level of agreement given that the allometric models are intended to provide broad approximations rather than exact values. However, reasons why some radionuclides deviate from what would be anticipated from Kleiber's law need to be determined to allow a more complete exploitation of the potential of allometric extrapolation within radioecological models. (orig.)

Glucagon-like Peptide 1 Conjugated to Recombinant Human Serum Albumin Variants with Modified Neonatal Fc Receptor Binding Properties. Impact on Molecular Structure and Half-Life

DEFF Research Database (Denmark)

Bukrinski, Jens T.; Sønderby, Pernille; Antunes, Filipa

2017-01-01

Glucagon-like peptide 1 (GLP-1) is a small incretin hormone stimulated by food intake, resulting in an amplification of the insulin response. Though interesting as a drug candidate for the treatment of type 2 diabetes mellitus, its short plasma half-life of less than 3 minutes limits its clinical...... use. A strategy to extend the half-life of GLP-1 utilizes the long half-life of human serum albumin (HSA) by combining the two via chemical conjugation or genetic fusion. HSA has a plasma half-life of around 21 days owing to its interaction with the neonatal Fc receptor (FcRn) expressed in endothelial...... with the available structural information on the FcRn and GLP-1 receptor (GLP-1R) obtained from X-ray crystallography, we can explain the observed in-vitro and in-vivo behaviour. We conclude that the conjugation of GLP-1 to rHSA does not affect the interaction between rHSA and FcRn, while the observed decrease...

Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification

KAUST Repository

Dineshram, R.

2015-10-28

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Decreasing pH due to anthropogenic CO2 inputs, called ocean acidification (OA), can make coastal environments unfavorable for oysters. This is a serious socioeconomical issue for China which supplies >70% of the world\\'s edible oysters. Here, we present an iTRAQ-based protein profiling approach for the detection and quantification of proteome changes under OA in the early life stage of a commercially important oyster, Crassostrea hongkongensis. Availability of complete genome sequence for the pacific oyster (Crassostrea gigas) enabled us to confidently quantify over 1500 proteins in larval oysters. Over 7% of the proteome was altered in response to OA at pHNBS 7.6. Analysis of differentially expressed proteins and their associated functional pathways showed an upregulation of proteins involved in calcification, metabolic processes, and oxidative stress, each of which may be important in physiological adaptation of this species to OA. The downregulation of cytoskeletal and signal transduction proteins, on the other hand, might have impaired cellular dynamics and organelle development under OA. However, there were no significant detrimental effects in developmental processes such as metamorphic success. Implications of the differentially expressed proteins and metabolic pathways in the development of OA resistance in oyster larvae are discussed. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD002138 (http://proteomecentral.proteomexchange.org/dataset/PXD002138).

Comparative and quantitative proteomics reveal the adaptive strategies of oyster larvae to ocean acidification

KAUST Repository

Dineshram, R.; Q., Quan; Sharma, Rakesh; Chandramouli, Kondethimmanahalli; Yalamanchili, Hari Krishna; Chu, Ivan; Thiyagarajan, Vengatesen

2015-01-01

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Decreasing pH due to anthropogenic CO2 inputs, called ocean acidification (OA), can make coastal environments unfavorable for oysters. This is a serious socioeconomical issue for China which supplies >70% of the world's edible oysters. Here, we present an iTRAQ-based protein profiling approach for the detection and quantification of proteome changes under OA in the early life stage of a commercially important oyster, Crassostrea hongkongensis. Availability of complete genome sequence for the pacific oyster (Crassostrea gigas) enabled us to confidently quantify over 1500 proteins in larval oysters. Over 7% of the proteome was altered in response to OA at pHNBS 7.6. Analysis of differentially expressed proteins and their associated functional pathways showed an upregulation of proteins involved in calcification, metabolic processes, and oxidative stress, each of which may be important in physiological adaptation of this species to OA. The downregulation of cytoskeletal and signal transduction proteins, on the other hand, might have impaired cellular dynamics and organelle development under OA. However, there were no significant detrimental effects in developmental processes such as metamorphic success. Implications of the differentially expressed proteins and metabolic pathways in the development of OA resistance in oyster larvae are discussed. The MS proteomics data have been deposited to the ProteomeXchange with identifiers PXD002138 (http://proteomecentral.proteomexchange.org/dataset/PXD002138).

Diagnosis of major depressive disorder by combining multimodal information from heart rate dynamics and serum proteomics using machine-learning algorithm.

Science.gov (United States)

Kim, Eun Young; Lee, Min Young; Kim, Se Hyun; Ha, Kyooseob; Kim, Kwang Pyo; Ahn, Yong Min

2017-06-02

Major depressive disorder (MDD) is a systemic and multifactorial disorder that involves abnormalities in multiple biochemical pathways and the autonomic nervous system. This study applied a machine-learning method to classify MDD and control groups by incorporating data from serum proteomic analysis and heart rate variability (HRV) analysis for the identification of novel peripheral biomarkers. The study subjects consisted of 25 drug-free female MDD patients and 25 age- and sex-matched healthy controls. First, quantitative serum proteome profiles were analyzed by liquid chromatography-tandem mass spectrometry using pooled serum samples from 10 patients and 10 controls. Next, candidate proteins were quantified with multiple reaction monitoring (MRM) in 50 subjects. We also analyzed 22 linear and nonlinear HRV parameters in 50 subjects. Finally, we identified a combined biomarker panel consisting of proteins and HRV indexes using a support vector machine with recursive feature elimination. A separation between MDD and control groups was achieved using five parameters (apolipoprotein B, group-specific component, ceruloplasmin, RMSSD, and SampEn) at 80.1% classification accuracy. A combination of HRV and proteomic data achieved better classification accuracy. A high classification accuracy can be achieved by combining multimodal information from heart rate dynamics and serum proteomics in MDD. Our approach can be helpful for accurate clinical diagnosis of MDD. Further studies using larger, independent cohorts are needed to verify the role of these candidate biomarkers for MDD diagnosis. Copyright © 2017 Elsevier Inc. All rights reserved.

Three examples of quantum dynamics on the half-line with smooth bouncing

Science.gov (United States)

Almeida, C. R.; Bergeron, H.; Gazeau, J.-P.; Scardua, A. C.

2018-05-01

This article is an introductory presentation of the quantization of the half-plane based on affine coherent states (ACS). The half-plane carries a natural affine symmetry, i.e. it is a homogeneous space for the 1d-affine group, and it is viewed as the phase space for the dynamics of a positive physical quantity evolving with time. Its affine symmetry is preserved due to the covariance of this type of quantization. We promote the interest of such a procedure for transforming a classical model into a quantum one, since the singularity at the origin is systematically removed, and the arbitrariness of boundary conditions for the Schrödinger operator can be easily overcome. We explain some important mathematical aspects of the method. Three elementary examples of applications are presented, the quantum breathing of a massive sphere, the quantum smooth bouncing of a charged sphere, and a smooth bouncing of "dust" sphere as a simple model of quantum Newtonian cosmology.

Proteomics Core

Data.gov (United States)

Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome

Science.gov (United States)

Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong

2013-01-01

We constructed and simulated a ‘minimal proteome’ model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that ‘proper’ populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643

Development of a time-variable nuclear pulser for half life measurements

International Nuclear Information System (INIS)

Zahn, Guilherme S.; Domienikan, Claudio; Carvalhaes, Roberto P. M.; Genezini, Frederico A.

2013-01-01

In this work a time-variable pulser system with an exponentially-decaying pulse frequency is presented, which was developed using the low-cost, open-source Arduino microcontroler plataform. In this system, the microcontroller produces a TTL signal in the selected rate and a pulse shaper board adjusts it to be entered in an amplifier as a conventional pulser signal; both the decay constant and the initial pulse rate can be adjusted using a user-friendly control software, and the pulse amplitude can be adjusted using a potentiometer in the pulse shaper board. The pulser was tested using several combinations of initial pulse rate and decay constant, and the results show that the system is stable and reliable, and is suitable to be used in half-life measurements.

Development of a time-variable nuclear pulser for half life measurements

Energy Technology Data Exchange (ETDEWEB)

Zahn, Guilherme S.; Domienikan, Claudio; Carvalhaes, Roberto P. M.; Genezini, Frederico A. [Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP. P.O. Box 11049, Sao Paulo, 05422-970 (Brazil)

2013-05-06

In this work a time-variable pulser system with an exponentially-decaying pulse frequency is presented, which was developed using the low-cost, open-source Arduino microcontroler plataform. In this system, the microcontroller produces a TTL signal in the selected rate and a pulse shaper board adjusts it to be entered in an amplifier as a conventional pulser signal; both the decay constant and the initial pulse rate can be adjusted using a user-friendly control software, and the pulse amplitude can be adjusted using a potentiometer in the pulse shaper board. The pulser was tested using several combinations of initial pulse rate and decay constant, and the results show that the system is stable and reliable, and is suitable to be used in half-life measurements.

A Proposal of the Ur-proteome

Science.gov (United States)

Palacios-Pérez, Miryam; Andrade-Díaz, Fernando; José, Marco V.

2017-11-01

Herein we outline a plausible proteome, encoded by assuming a primeval RNY genetic code. We unveil the primeval phenotype by using only the RNA genotype; it means that we recovered the most ancestral proteome, mostly made of the 8 amino acids encoded by RNY triplets. By looking at those fragments, it is noticeable that they are positioned, not at catalytic sites, but in the cofactor binding sites. It implies that the stabilization of a molecule appeared long before its catalytic activity, and therefore the Ur-proteome comprised a set of proteins modules that corresponded to Cofactor Stabilizing Binding Sites (CSBSs), which we call the primitive bindome. With our method, we reconstructed the structures of the "first protein modules" that Sobolevsky and Trifonov (2006) found by using only RMSD. We also examine the probable cofactors that bound to them. We discuss the notion of CSBSs as the first proteins modules in progenotes in the context of several proposals about the primitive forms of life.

Arabidopsis Regenerating Protoplast: A Powerful Model System for Combining the Proteomics of Cell Wall Proteins and the Visualization of Cell Wall Dynamics

OpenAIRE

Yokoyama, Ryusuke; Kuki, Hiroaki; Kuroha, Takeshi; Nishitani, Kazuhiko

2016-01-01

The development of a range of sub-proteomic approaches to the plant cell wall has identified many of the cell wall proteins. However, it remains difficult to elucidate the precise biological role of each protein and the cell wall dynamics driven by their actions. The plant protoplast provides an excellent means not only for characterizing cell wall proteins, but also for visualizing the dynamics of cell wall regeneration, during which cell wall proteins are secreted. It therefore offers a uni...

An Overview of Advanced SILAC-Labeling Strategies for Quantitative Proteomics.

Science.gov (United States)

Terzi, F; Cambridge, S

2017-01-01

Comparative, quantitative mass spectrometry of proteins provides great insight to protein abundance and function, but some molecular characteristics related to protein dynamics are not so easily obtained. Because the metabolic incorporation of stable amino acid isotopes allows the extraction of distinct temporal and spatial aspects of protein dynamics, the SILAC methodology is uniquely suited to be adapted for advanced labeling strategies. New SILAC strategies have emerged that allow deeper foraging into the complexity of cellular proteomes. Here, we review a few advanced SILAC-labeling strategies that have been published during last the years. Among them, different subsaturating-labeling as well as dual-labeling schemes are most prominent for a range of analyses including those of neuronal proteomes, secretion, or cell-cell-induced stimulations. These recent developments suggest that much more information can be gained from proteomic analyses if the labeling strategies are specifically tailored toward the experimental design. © 2017 Elsevier Inc. All rights reserved.

Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise.

Science.gov (United States)

Camera, Donny M; Burniston, Jatin G; Pogson, Mark A; Smiles, William J; Hawley, John A

2017-12-01

It is generally accepted that muscle adaptation to resistance exercise (REX) training is underpinned by contraction-induced, increased rates of protein synthesis and dietary protein availability. By using dynamic proteome profiling (DPP), we investigated the contribution of both synthesis and breakdown to changes in abundance on a protein-by-protein basis in human skeletal muscle. Age-matched, overweight males consumed 9 d of a high-fat, low-carbohydrate diet during which time they either undertook 3 sessions of REX or performed no exercise. Precursor enrichment and the rate of incorporation of deuterium oxide into newly synthesized muscle proteins were determined by mass spectrometry. Ninety proteins were included in the DPP, with 28 proteins exhibiting significant responses to REX. The most common pattern of response was an increase in turnover, followed by an increase in abundance with no detectable increase in protein synthesis. Here, we provide novel evidence that demonstrates that the contribution of synthesis and breakdown to changes in protein abundance induced by REX differ on a protein-by-protein basis. We also highlight the importance of the degradation of individual muscle proteins after exercise in human skeletal muscle.-Camera, D. M., Burniston, J. G., Pogson, M. A., Smiles, W. J., Hawley, J. A. Dynamic proteome profiling of individual proteins in human skeletal muscle after a high-fat diet and resistance exercise. © FASEB.

Analysis of existing data and specification of an experiment to determine the 252Cf half-life to the required degree of accuracy

International Nuclear Information System (INIS)

Lorenz, A.; Kharitonov, I.A.

1994-02-01

The methods used and the results obtained in measurements of the 252 Cf half-life are analyzed. In calculating the weighted mean value, additional error components as well as those given by the authors are taken into account. In order to reduce the error in the weighted mean value to less than 0.1%, the need and the requirements for an exact measurement are specified. A half-life of 2.6473±0.0028 years is recommended. (author). 16 refs, 3 tabs

Innovative methodology for intercomparison of radionuclide calibrators using short half-life in situ prepared radioactive sources

International Nuclear Information System (INIS)

Oliveira, P. A.; Santos, J. A. M.

2014-01-01

Purpose: An original radionuclide calibrator method for activity determination is presented. The method could be used for intercomparison surveys for short half-life radioactive sources used in Nuclear Medicine, such as 99m Tc or most positron emission tomography radiopharmaceuticals. Methods: By evaluation of the resulting net optical density (netOD) using a standardized scanning method of irradiated Gafchromic XRQA2 film, a comparison of the netOD measurement with a previously determined calibration curve can be made and the difference between the tested radionuclide calibrator and a radionuclide calibrator used as reference device can be calculated. To estimate the total expected measurement uncertainties, a careful analysis of the methodology, for the case of 99m Tc, was performed: reproducibility determination, scanning conditions, and possible fadeout effects. Since every factor of the activity measurement procedure can influence the final result, the method also evaluates correct syringe positioning inside the radionuclide calibrator. Results: As an alternative to using a calibrated source sent to the surveyed site, which requires a relatively long half-life of the nuclide, or sending a portable calibrated radionuclide calibrator, the proposed method uses a source preparedin situ. An indirect activity determination is achieved by the irradiation of a radiochromic film using 99m Tc under strictly controlled conditions, and cumulated activity calculation from the initial activity and total irradiation time. The irradiated Gafchromic film and the irradiator, without the source, can then be sent to a National Metrology Institute for evaluation of the results. Conclusions: The methodology described in this paper showed to have a good potential for accurate (3%) radionuclide calibrators intercomparison studies for 99m Tc between Nuclear Medicine centers without source transfer and can easily be adapted to other short half-life radionuclides

Study of the Bs meson and measurement of its half-life with the ALEPH detector

International Nuclear Information System (INIS)

Duarte, H.

1994-01-01

The B s 0 meson is the bound state of a quark anti-quark pair made up of a beauty particle and a strange particle. In the first chapter we review different experimental results leading to the existence of B S 0 meson and we draw the theoretical framework of the concept of beauty particles. The second chapter deals with the probability of the formation of a meson containing a strange quark during the fragmentation. This chapter also contains a re-analysis of the whole data constraining the mixing parameter B s 0 -B s 0 -bar. The relevancy of the analysis relies on the assumption that the B s 0 meson decays only into one D s , one lepton and one neutrino. The ALEPH detector is described in chapter 3, this four-pi, multi-particle detector is installed on the e + e - LEP (Large Electron Positron Collider). The signature selected for the measurement of the half-life is the combination of one D s in the decay modes: φπ, K *0 K with a lepton having opposite charge. This measurement implies the knowledge of the B s 0 momentum and of its flight length. In order to assess the momentum of the neutrino, a technique of measuring missing energy is presented in the chapter 4. The selection of B s 0 events is detailed in the chapter 5. A cutting limit on the energy of B s 0 based on the missing energy is used to deduce the production rate of B s 0 . In the chapter 6 we present the measurement of the half-life of B s 0 , the method used for the reconstruction of decay vertices and of the event main vertex is detailed. The validity of the method has been tested on Monte-Carlo simulations. The final result concerning the measurement of the half-life is: τ(B s )=[1.92(+0.45-0.35)±0.04] ps [fr

Hair-to-blood ratio and biological half-life of mercury: experimental study of methylmercury exposure through fish consumption in humans.

Science.gov (United States)

Yaginuma-Sakurai, Kozue; Murata, Katsuyuki; Iwai-Shimada, Miyuki; Nakai, Kunihiko; Kurokawa, Naoyuki; Tatsuta, Nozomi; Satoh, Hiroshi

2012-02-01

The hair-to-blood ratio and biological half-life of methylmercury in a one-compartment model seem to differ between past and recent studies. To reevaluate them, 27 healthy volunteers were exposed to methylmercury at the provisional tolerable weekly intake (3.4 µg/kg body weight/week) for adults through fish consumption for 14 weeks, followed by a 15-week washout period after the cessation of exposure. Blood was collected every 1 or 2 weeks, and hair was cut every 4 weeks. Total mercury (T-Hg) concentrations were analyzed in blood and hair. The T-Hg levels of blood and hair changed with time (p < 0.001). The mean concentrations increased from 6.7 ng/g at week 0 to 26.9 ng/g at week 14 in blood, and from 2.3 to 8.8 µg/g in hair. The mean hair-to-blood ratio after the adjustment for the time lag from blood to hair was 344 ± 54 (S.D.) for the entire period. The half-lives of T-Hg were calculated from raw data to be 94 ± 23 days for blood and 102 ± 31 days for hair, but the half-lives recalculated after subtracting the background levels from the raw data were 57 ± 18 and 64 ± 22 days, respectively. In conclusion, the hair-to-blood ratio of methylmercury, based on past studies, appears to be underestimated in light of recent studies. The crude half-life may be preferred rather than the recalculated one because of the practicability and uncertainties of the background level, though the latter half-life may approximate the conventional one.

RBC-/Cr-51/ half-life and albumin turnover in growing Beagle dogs during chronic radial acceleration

Science.gov (United States)

Beckman, D. A.; Evans, J. W.; Oyama, J.

1979-01-01

The effects of chronic centrifugation on growing Beagle dogs exposed to -2 or -2.6 Gx on albumin and RBC turnover rates, albumin concentration and space, and total blood volume were determined and compared with caged and run control of animals. Albumin-(I-125) and autologous RBC-(Cr-51) preparations were injected into all dogs at day 82 of the centrifugation periods, and the disappearance curves were determined by successive bleedings of the animals over the next 35 d, during which the centrifugation was continued. There were no differences in albumin turnover rates or space. Two populations of RBCs were found in both centrifugated groups, one with a normal half-life of 27 + or - 1 S.E.M. d, and one with a significantly (p less than 0.01) shorter half-life of 15 + or - 2 S.E.M. d. An absolute polycythemia was also observed in both centrifuged groups. The results suggest that chronic centrifugation acts through some as-yet unknown mechanism to affect RBC population kinetics.

Goiania radiation accident: 30 years - a half-life for a whole life..

International Nuclear Information System (INIS)

Reis, R.G.; Lucena, E.A.; Arantes, R.R.; Silva, A.A.; Reis, A.A.

2017-01-01

The radiological accident in Goiânia, Brazil, considered the largest urban radiological accident in the world, generated several publications in the technical area that are widely disseminated in the scientific literature, given the importance of the lessons learned. However, in a simple conversation with people who worked on that accident, it is noted that many reports have not been recorded. In this year in which 30 years of the event is completed, it will be of great value to record personal testimonies that are not in technical or scientific books. And what can we tell after a half-life that lasted for a lifetime? The lived stories, the situations, the improvisations, the way to solve, the overcoming, the human side, the emotions, happy or sad, short or long, funny or not. The objective of this work is to preserve, maintain and divulge reports and situations experienced by people who worked on the radiological accident with Cs-137 in Goiânia. Audio or video recordings about experiences lived in Goiânia by people who worked in that emergency situation were carried out. The reports are free and the form of registration is always at the discretion of the narrator. Storing records allows to preserve, maintain, and disclose the accident to other generations

Elucidating Host-Pathogen Interactions Based on Post-Translational Modifications Using Proteomics Approaches

DEFF Research Database (Denmark)

Ravikumar, Vaishnavi; Jers, Carsten; Mijakovic, Ivan

2015-01-01

can be efficiently applied to gain an insight into the molecular mechanisms involved. The measurement of the proteome and post-translationally modified proteome dynamics using mass spectrometry, results in a wide array of information, such as significant changes in protein expression, protein...... display host specificity through a complex network of molecular interactions that aid their survival and propagation. Co-infection states further lead to complications by increasing the microbial burden and risk factors. Quantitative proteomics based approaches and post-translational modification analysis...... pathogen interactions....

Thirty years after Chernobyl: Long-term determination of 137Cs effective half-life in the lichen Stereocaulon vesuvianum.

Science.gov (United States)

Savino, F; Pugliese, M; Quarto, M; Adamo, P; Loffredo, F; De Cicco, F; Roca, V

2017-06-01

It has been widely shown that nuclear fallout includes substances, which accumulate in organisms such as crustaceans, fish, mushrooms and lichens, helping to evaluate the activity concentration of contaminants accumulated on a long time. In this context, radiocaesium deposited in soil following the Chernobyl accident on 26 April 1986 is known to have remained persistently available for plant uptake in many areas of Europe. Studies on the lichen Stereocaulon vesuvianum show the plant's high capacity to retain radionuclides from the substrate and the air. After the Chernobyl accident, starting from September 1986, at the Radioactivity Laboratory (LaRa) of the University of Naples Federico II, four monitoring campaigns to evaluate the activity concentration of four isotopes of the two elements caesium and ruthenium ( 134 Cs, 137 Cs, 103 Ru and 106 Ru) were carried out until 1999. This study allowed the effective half-life of 134 Cs and 137 Cs to be estimated. Twenty-eight years after the accident, in December 2014, a further sampling was carried out; only 137 Cs was revealed beyond the detection limits, measuring activity concentrations ranging from 20 to 40 Bq/kg, while the other radionuclides were no longer observed due to their shorter half-life. The last sampling allowed more precise determination of the effective half-life of 137 Cs (6.2 ± 0.1 year), due to the larger dataset on a large time period. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mapping out starvation responses in yeast by proteomics

DEFF Research Database (Denmark)

Rødkær, Steven Vestergaard; Færgeman, Nils J.; Andersen, Jens S.

2011-01-01

that are involved in this positive outcome. Based on that, processes like autophagy, lipid turnover and the generation/clearance of reactive oxygen species (ROS) have all been describe to affect life span, either alone, or in a not fully characterized interplay. The baker’s yeast Saccharomyces cerevisae is by now...... the organism with the best characterized proteome and is therefore the organism of choice in many proteomic studies. Additionally, this single-celled organism exhibits many conserved proteins and pathways of higher animals, thus observations in the yeast might reveal important information applying to other...

Preliminary measurements of the 87Rb half-life by means of the needle counter

International Nuclear Information System (INIS)

Zastawny, A.; Rabsztyn, B.

1989-01-01

In order to test the detector and to obtain the experience before starting the exact measurements, the measurements of 87 Rb half-life have been made. RbNO 3 produced by Merck was used to prepare the samples. The samples were prepared by evaporation of RbNO 3 water solution on an aluminium foil of 2,9 mg/cm 2 . The water solutions were changed in the range from (3286,4±1,8) x 10 -6 to (480,85±0,3) x 10 -6 . The background of the aluminium foil was equal to (0,117±0,007) cpm. In other measurements the back-scattering effect of 87 Rb beta rays on the aluminium foil amounted to 4%, as the measurements were performed in the 2π geometry. The diameters of samples were about 10 mm. The specific radioactivities of samples were measured versus the surface changed in the range (60-320) μg/cm 2 . The extrapolated value of the half-life, corrected for the chemical purity of the compound (as declared by the manufacterer) is equal to (4,86±0,1) x 10 10 years. This value is in good agreement with commonly accepted value of 4,88 x 10 10 years and with another last measurements. 10 refs., 1 fig., 2 tabs. (author)

Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle.

Directory of Open Access Journals (Sweden)

Jacob R Waldbauer

Full Text Available BACKGROUND: Growth of the ocean's most abundant primary producer, the cyanobacterium Prochlorococcus, is tightly synchronized to the natural 24-hour light-dark cycle. We sought to quantify the relationship between transcriptome and proteome dynamics that underlie this obligate photoautotroph's highly choreographed response to the daily oscillation in energy supply. METHODOLOGY/PRINCIPAL FINDINGS: Using RNA-sequencing transcriptomics and mass spectrometry-based quantitative proteomics, we measured timecourses of paired mRNA-protein abundances for 312 genes every 2 hours over a light-dark cycle. These temporal expression patterns reveal strong oscillations in transcript abundance that are broadly damped at the protein level, with mRNA levels varying on average 2.3 times more than the corresponding protein. The single strongest observed protein-level oscillation is in a ribonucleotide reductase, which may reflect a defense strategy against phage infection. The peak in abundance of most proteins also lags that of their transcript by 2-8 hours, and the two are completely antiphase for some genes. While abundant antisense RNA was detected, it apparently does not account for the observed divergences between expression levels. The redirection of flux through central carbon metabolism from daytime carbon fixation to nighttime respiration is associated with quite small changes in relative enzyme abundances. CONCLUSIONS/SIGNIFICANCE: Our results indicate that expression responses to periodic stimuli that are common in natural ecosystems (such as the diel cycle can diverge significantly between the mRNA and protein levels. Protein expression patterns that are distinct from those of cognate mRNA have implications for the interpretation of transcriptome and metatranscriptome data in terms of cellular metabolism and its biogeochemical impact.

Nonautonomous dynamical systems in the life sciences

CERN Document Server

Pötzsche, Christian

2013-01-01

Nonautonomous dynamics describes the qualitative behavior of evolutionary differential and difference equations, whose right-hand side is explicitly time dependent. Over recent years, the theory of such systems has developed into a highly active field related to, yet recognizably distinct from that of classical autonomous dynamical systems. This development was motivated by problems of applied mathematics, in particular in the life sciences where genuinely nonautonomous systems abound. The purpose of this monograph is to indicate through selected, representative examples how often nonautonomous systems occur in the life sciences and to outline the new concepts and tools from the theory of nonautonomous dynamical systems that are now available for their investigation.

Accurate γ-ray spectrometry measurements of the half-life of 92Sr

International Nuclear Information System (INIS)

Leconte, P.; Hudelot, J.P.; Antony, M.

2008-01-01

Studies of the nuclear fuel cycle require an accurate knowledge of the energy release from the decay of radioactive nuclides produced in a reactor, including precise half-life data for the short-lived radionuclides. Moreover, short-lived fission products are crucial for fission rate distribution measurements performed in low-power facilities, such as EOLE and MINERVE of CEA Cadarache [Fougeras, P., 2005. EOLE, MINERVE and MASURCA facilities and their associated neutron experimental programs. In: 13th International Conference on Nuclear Engineering, Beijing, China, 16-20 May 2005], and their nuclear decay data need to be known to high precision. For these reasons, the half-life of 92 Sr has been measured to solve a recently observed inconsistency identified with the quoted value in the main nuclear applications libraries (including JEFF3.1): T 1/2 =2.71±0.01 h [Parsa, B., Ashari, A., Goolvard, L., Nobar, Y.M., 1971. Decay scheme of 2.71 h 92 Sr. Nucl. Phys. A 175, 629-640]. An overestimation of 4.5% has been identified in this work, based on two independent methods. Specific γ-ray spectrometry measurements on activated fissile foils have been carried out, using two HPGe detectors. Influencing factors such as net area measurements of photopeaks, pulse pile-up accuracy and dead time corrections in the presence of decaying activity are discussed. A new value has been obtained by combining eight series of measurements: T 1/2 =2.594±0.006 h. The uncertainty has been reduced by a factor of two with respect to previous evaluations. This measured value also shows good agreement with the most recent studies of T 1/2 =2.627±0.009 h [Nir-El, Y., 2003. Private Communications. Soreq Research Centre, Yavne, Israel

Clinical proteomics

DEFF Research Database (Denmark)

Albrethsen, Jakob; Frederiksen, Hanne; Johannsen, Trine Holm

2018-01-01

Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS)-platforms...... standards and calibrants. The present challenge is to examine if targeted proteomics of IGF-I can truly measure up to the routine performance that must be expected from a clinical testing platform.......Clinical proteomics aims to deliver cost-effective multiplexing of potentially hundreds of diagnostic proteins, including distinct protein isoforms. The analytical strategy known as targeted proteomics is particularly promising because it is compatible with robust mass spectrometry (MS......)-platforms already implemented in many clinical laboratories for routine quantitation of small molecules (i.e. uHPLC coupled to triple-quadrupole MS). Progress in targeted proteomics of circulating insulin-like growth factor 1 (IGF-I) have provided valuable insights about tryptic peptides, transitions, internal...

Halobacterium salinarum NRC-1 PeptideAtlas: strategies for targeted proteomics

Science.gov (United States)

Van, Phu T.; Schmid, Amy K.; King, Nichole L.; Kaur, Amardeep; Pan, Min; Whitehead, Kenia; Koide, Tie; Facciotti, Marc T.; Goo, Young-Ah; Deutsch, Eric W.; Reiss, David J.; Mallick, Parag; Baliga, Nitin S.

2009-01-01

The relatively small numbers of proteins and fewer possible posttranslational modifications in microbes provides a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a Peptide Atlas (PA) for 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636,000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has helped highlight plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics. PMID:18652504

Lithium as an adjunct to radioiodine therapy in Graves' disease for prolonging the intrathyroidal effective half-life of radioiodine. Useful or not?

Energy Technology Data Exchange (ETDEWEB)

Dunkelmann, S.; Kuenstner, H.; Nabavi, E.; Eberlein, U.; Groth, P.; Schuemichen, C. [Rostock Univ. (Germany). Klinik und Poliklinik fuer Nuklearmedizin, Zentrum fuer Radiologie

2006-07-01

Aim: Evaluation of intrathyroidal kinetics of radioiodine with and without lithium as adjunct with respect to the increase in radiation dose delivered to the thyroid. Patients, methods: 267 patients in three groups were included in the study. Group I with 227 patients served as control group, Group II with 21 patients and Group III with 19 patients were distinguished by an intrathyroidal half-life of radioiodine below 3.5 days in the diagnostic test. Patients in Group III received 885 mg lithium carbonate a day for 2 weeks as adjunct to radioiodine therapy. Both diagnostic and therapeutic radioiodine kinetics were followed up by at least 10 uptake measurements within a minimum of 48 h. Kinetics of radioiodine were defined mathematically as balance of the thyroidal iodine intake and excretion by a two-compartment model. Results: Under therapy the maximum uptake of radioiodine was reduced by nearly 10% in all groups, in Group I, the effective half-life as well as the product of maximum uptake x effective half-life as an equivalent of radiation dose independent of thyroid volume was lowered in the same magnitude. In Group II, the energy-dose equivalent remained constant under therapy. With adjunct lithium in Group III, the effective half-life was prolonged significantly by factor 1.61{+-}0.49 and the volume-independent energy-dose equivalent by factor 1.39{+-}0.37. No severe side effects of lithium were observed. Conclusion: Using lithium as adjunct to radio-iodine therapy increases the radiation dose delivered to the thyroid by 39% on average and nearly 30% of radioiodine activity can be saved in these patients. Lithium is recommended in patients with very short effective half-life in the diagnostic test in order to reduce the activity required and whole-body radiation dose. (orig.)

The Half Life of the 53 keV Level in {sup 197}Pt

Energy Technology Data Exchange (ETDEWEB)

Malmskog, S G

1967-02-15

The half life of the recently proposed 53 keV level in {sup 197}Pt has been measured to 18.5 {+-} 1.5 nsec using the delayed coincidence technique. This level, which is identified with the f{sub 5/2} single particle state, decays directly to the p{sub 1/2} ground state in {sup 197}Pt. The reduced E2 transition probability for this 53 keV transition has been deduced and compared with the results obtained for the corresponding transitions in other Pt, Hg, and Pb isotopes and with the theoretical predictions by Sorensen and by Wahlborn and Martinson.

First 0ν half-life limit from the Gotthard xenon time projection chamber

International Nuclear Information System (INIS)

Wong, H.T.; Boehm, F.; Fisher, P.

1991-01-01

A xenon Time Projection Chamber with an active volume of 207 liters has been built to study 0ν and 2ν double beta decay in 136 Xe. The TPC has been installed in the Gotthard Tunnel Underground Laboratory, and is currently taking data with 5 atm of xenon enriched in 62.5% 136 Xe. The first 166 hours of data are presented. Based on this data set, we deduce a half-life limit of T(0 + → 0 + ) > 6.2 x 10 21 years for the 0ν mode, at a 90% C.L. (author)

A Two-pronged Binding Mechanism of IgG to the Neonatal Fc Receptor Controls Complex Stability and IgG Serum Half-life

DEFF Research Database (Denmark)

Jensen, Pernille Foged; Schoch, Angela; Larraillet, Vincent

2017-01-01

The success of recombinant monoclonal immunoglobulins (IgG) is rooted in their ability to target distinct antigens with high affinity combined with an extraordinarily long serum half-life, typically around 3 weeks. The pharmacokinetics of IgGs is intimately linked to the recycling mechanism...... half-life of ∼8 days. Here we dissect the molecular origins of excessive FcRn binding in therapeutic IgGs using a combination of hydrogen/deuterium exchange mass spectrometry and FcRn affinity chromatography. We provide experimental evidence for a two-pronged IgG-FcRn binding mechanism involving direct...

Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome

Science.gov (United States)

Kosová, Klára; Vítámvás, Pavel; Urban, Milan O.; Prášil, Ilja T.; Renaut, Jenny

2018-01-01

HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic

Serum proteome profiling in canine idiopathic dilated cardiomyopathy using TMT-based quantitative proteomics approach.

Science.gov (United States)

Bilić, Petra; Guillemin, Nicolas; Kovačević, Alan; Beer Ljubić, Blanka; Jović, Ines; Galan, Asier; Eckersall, Peter David; Burchmore, Richard; Mrljak, Vladimir

2018-05-15

Idiopathic dilated cardiomyopathy (iDCM) is a primary myocardial disorder with an unknown aetiology, characterized by reduced contractility and ventricular dilation of the left or both ventricles. Naturally occurring canine iDCM was used herein to identify serum proteomic signature of the disease compared to the healthy state, providing an insight into underlying mechanisms and revealing proteins with biomarker potential. To achieve this, we used high-throughput label-based quantitative LC-MS/MS proteomics approach and bioinformatics analysis of the in silico inferred interactome protein network created from the initial list of differential proteins. To complement the proteomic analysis, serum biochemical parameters and levels of know biomarkers of cardiac function were measured. Several proteins with biomarker potential were identified, such as inter-alpha-trypsin inhibitor heavy chain H4, microfibril-associated glycoprotein 4 and apolipoprotein A-IV, which were validated using an independent method (Western blotting) and showed high specificity and sensitivity according to the receiver operating characteristic curve analysis. Bioinformatics analysis revealed involvement of different pathways in iDCM, such as complement cascade activation, lipoprotein particles dynamics, elastic fibre formation, GPCR signalling and respiratory electron transport chain. Idiopathic dilated cardiomyopathy is a severe primary myocardial disease of unknown cause, affecting both humans and dogs. This study is a contribution to the canine heart disease research by means of proteomic and bioinformatic state of the art analyses, following similar approach in human iDCM research. Importantly, we used serum as non-invasive and easily accessible biological source of information and contributed to the scarce data on biofluid proteome research on this topic. Bioinformatics analysis revealed biological pathways modulated in canine iDCM with potential of further targeted research. Also, several

A new simplified allometric approach for predicting the biological half-life of radionuclides in reptiles

International Nuclear Information System (INIS)

Beresford, N.A.; Wood, M.D.

2014-01-01

A major source of uncertainty in the estimation of radiation dose to wildlife is the prediction of internal radionuclide activity concentrations. Allometric (mass-dependent) relationships describing biological half-life (T 1/2b ) of radionuclides in organisms can be used to predict organism activity concentrations. The establishment of allometric expressions requires experimental data which are often lacking. An approach to predict the T 1/2b in homeothermic vertebrates has recently been proposed. In this paper we have adapted this to be applicable to reptiles. For Cs, Ra and Sr, over a mass range of 0.02–1.5 kg, resultant predictions were generally within a factor of 6 of reported values demonstrating that the approach can be used when measured T 1/2b data are lacking. However, the effect of mass on reptilian radionuclide T 1/2b is minimal. If sufficient measured data are available for a given radionuclide then it is likely that these would give a reasonable estimate of T 1/2b in any reptile species. - Highlights: • An allometric approach to predict radionuclide T 1/2b values in reptiles is derived. • Predictions are generally within a factor of six of measured values. • Radionuclide biological half-life is in-effect mass independent

Chromosomocentric approach to overcoming difficulties in implementation of international project Human Proteome

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A. I. Archakov

2013-12-01

Full Text Available The international project Human Proteome (PHP, being a logical continuation of the project Human Genome, was started on September 23, 2010. In correspondence with the genocentric approach, the PHP aim is to prepare a catalogue of all human proteins and to decipher a network of their interactions. The PHP implementation difficulties arise because the research subject itself – proteome – is much more complicated than genome. The major problem is the insufficient sensitivity of proteome methods that does not allow detecting low- and ultralow-copy proteins. Bad reproducibility of proteome methods and the lack of so-called “gold standard” is the second major complicacy in PHP implementation. The third problem is the dynamic character of proteome, its instabili­ty in time. The paper deals with possible variants of overcoming these complicacies, preventing from successful implementation of PHP.

Soybean Proteome Database 2012: Update on the comprehensive data repository for soybean proteomics

Directory of Open Access Journals (Sweden)

Hajime eOhyanagi

2012-05-01

Full Text Available The Soybean Proteome Database (SPD was created to provide a data repository for functional analyses of soybean responses to flooding stress, thought to be a major constraint for establishment and production of this plant. Since the last publication of the SPD, we thoroughly enhanced the contents of database, particularly protein samples and their annotations from several organelles. The current release contains 23 reference maps of soybean (Glycine max cv. Enrei proteins collected from several organs, tissues and organelles including the maps for plasma membrane, cell wall, chloroplast and mitochondrion, which were electrophoresed on two-dimensional polyacrylamide gels. Furthermore, the proteins analyzed with gel-free proteomics technique have been added and available online. In addition to protein fluctuations under flooding, those of salt and drought stress have been included in the current release. An omics table also has been provided to reveal relationships among mRNAs, proteins and metabolites with a unified temporal-profile tag in order to facilitate retrieval of the data based on the temporal profiles. An intuitive user interface based on dynamic HTML enables users to browse the network as well as the profiles of multiple omes in an integrated fashion. The SPD is available at: http://proteome.dc.affrc.go.jp/Soybean/.

On the way to high-power linear proton accelerator for the long half-life radionuclides transmutation

International Nuclear Information System (INIS)

Batskikh, G.I.; Lupandin, O.S.; Murin, B.P.; Fedotov, A.P.

1991-01-01

The concept of continuous mode high-power linear proton accelerator with 1.5 GeV energy, 0.3 A current for the long half-life nuclides transmutation into the short ones (waste of atomic power plants (APP)) is proposed. The accelerator design main principles, scheme and parameters are presented. The accent is made on the accelerator efficiency, reliability and radiation purity. (author)

Shared and Unique Proteins in Human, Mouse and Rat Saliva Proteomes: Footprints of Functional Adaptation

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Robert C. Karn

2013-12-01

Full Text Available The overall goal of our study was to compare the proteins found in the saliva proteomes of three mammals: human, mouse and rat. Our first objective was to compare two human proteomes with very different analysis depths. The 89 shared proteins in this comparison apparently represent a core of highly-expressed human salivary proteins. Of the proteins unique to each proteome, one-half to 2/3 lack signal peptides and probably are contaminants instead of less highly-represented salivary proteins. We recently published the first rodent saliva proteomes with saliva collected from the genome mouse (C57BL/6 and the genome rat (BN/SsNHsd/Mcwi. Our second objective was to compare the proteins in the human proteome with those we identified in the genome mouse and rat to determine those common to all three mammals, as well as the specialized rodent subset. We also identified proteins unique to each of the three mammals, because differences in the secreted protein constitutions can provide clues to differences in the evolutionary adaptation of the secretions in the three different mammals.

[Proteomics and its application to determine mechanism of action of traditional Chinese medicine].

Science.gov (United States)

Xin, Ping; Kuang, Hai-Xue; Li, Xiao-Liang; Wang, Yu; Zhang, Ben-Mei; Bu, He; Wang, Zhi-Bin; Meng, Yong-Hai; Wang, Yan-Hong; Wang, Qiu-Hong

2018-03-01

There is no doubt that the traditional Chinese medicine(TCM) is effective, practical and scientific after it was used for thousands of years. However, the mechanisms of action of many TCM are still unclear because of their multi-component, multi-target and multi-level features, which hinder the modernization and internationalization of the TCM. Proteomics is to analyze the composition and activity of intracellular proteins which are changing dynamically from a holistic perspective. It is consistent with the holistic and dynamic views of the TCM and brings about the hope of clarifying the mechanism of action of the TCM. In recent years, great progress has been made in the application of proteomics to determine the mechanism of the TCM. This article introduced the core technologies of proteomics and systematically summarized the applications of proteomics in the study of the mechanism of the Chinese medicinal formulae, single Chinese medicine and monomeric compounds from the TCM to provide innovative ideas and methods for reference. Copyright© by the Chinese Pharmaceutical Association.

Isolation of human anti-serum albumin Fab antibodies with an extended serum-half life.

Science.gov (United States)

Kang, Hyeon-Ju; Kim, Hye-Jin; Cha, Sang-Hoon

2016-01-01

The serum albumin (SA) has been exploited to generate long-acting biotherapeutics by taking advantage of the FcRn-mediated recycling mechanism in a direct or an indirect way. Since Fab fragments have been proven to be clinically safe for human usage, we assumed that human anti-SA Fab antibodies could have a great potential as a carrier molecule to extend the serum half-life of therapeutic proteins. We, herein, had attempted to isolate anti-SA Fab antibodies from HuDVFab-8L antibody library via a phage display technology, and identified eight discrete human Fab antibodies. One of the Fab antibodies, SL335, showed the strongest binding reactivity to human SA with nM range of affinity at both pH 6 and pH 7.4, and cross-reacted to SAs from various species including rat, mouse, canine and monkey. The in vivo pharmacokinetic assay using a rat model indicated that SL335 has approximately 10 fold longer serum half-life and 26 to 44-fold increase in AUC0 → ∞ compared to the negative control Fab molecule in both intravenous and subcutaneous administrations. Knowing that Fabs have proven to be safe in clinics for a long time, SL335 seems to have a great potential in generating long-acting protein drugs by tagging effector molecules with either chemical conjugation or genetic fusion. Copyright © 2015 Elsevier B.V. All rights reserved.

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression.

Science.gov (United States)

Megger, Dominik A; Philipp, Jos; Le-Trilling, Vu Thuy Khanh; Sitek, Barbara; Trilling, Mirko

2017-01-01

Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus.

Deciphering of the Human Interferon-Regulated Proteome by Mass Spectrometry-Based Quantitative Analysis Reveals Extent and Dynamics of Protein Induction and Repression

Directory of Open Access Journals (Sweden)

Dominik A. Megger

2017-09-01

Full Text Available Interferons (IFNs are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction. In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive analysis revealed important insights into the human IFN-regulated proteome and its dynamics of protein induction and repression. Interestingly, the new class of IFN-repressed genes comprises known host factors for highly relevant pathogens such as HIV, dengue virus, and hepatitis C virus.

Precision half-life determination of a mirror β transition: The decay of 31S

International Nuclear Information System (INIS)

Bacquias, A.; Kurtukian-Nieto, T.; Ascher, P.; Audirac, L.; Blank, B.; Giovinazzo, J.; Aeystoe, J.; Elomaa, V.V.; Eronen, T.; Hakala, J.; Jokinen, A.; Kankainen, A.; Karvonen, P.; Kolhinen, V.S.; Moore, I.D.; Rahaman, S.; Reponen, M.; Rissanen, J.; Saastamoinen, A.; Souin, J.

2012-01-01

The half-life of the mirror β decay of 31 S has been measured at the IGISOL facility at the University of Jyvaeskylae. The value obtained is T 1/2 ( 31 S)=(2553.4±1.8) ms, in agreement with previous measurements, but with a precision that is better by a factor of ten than the literature value previously adopted. When the new result is combined with the Q EC value measured recently at JYFLTRAP, a precision of better than 10 -3 is obtained for the ft value. (orig.)

Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

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Klipp Edda

2006-12-01

Full Text Available Abstract Background Translating a known metabolic network into a dynamic model requires reasonable guesses of all enzyme parameters. In Bayesian parameter estimation, model parameters are described by a posterior probability distribution, which scores the potential parameter sets, showing how well each of them agrees with the data and with the prior assumptions made. Results We compute posterior distributions of kinetic parameters within a Bayesian framework, based on integration of kinetic, thermodynamic, metabolic, and proteomic data. The structure of the metabolic system (i.e., stoichiometries and enzyme regulation needs to be known, and the reactions are modelled by convenience kinetics with thermodynamically independent parameters. The parameter posterior is computed in two separate steps: a first posterior summarises the available data on enzyme kinetic parameters; an improved second posterior is obtained by integrating metabolic fluxes, concentrations, and enzyme concentrations for one or more steady states. The data can be heterogenous, incomplete, and uncertain, and the posterior is approximated by a multivariate log-normal distribution. We apply the method to a model of the threonine synthesis pathway: the integration of metabolic data has little effect on the marginal posterior distributions of individual model parameters. Nevertheless, it leads to strong correlations between the parameters in the joint posterior distribution, which greatly improve the model predictions by the following Monte-Carlo simulations. Conclusion We present a standardised method to translate metabolic networks into dynamic models. To determine the model parameters, evidence from various experimental data is combined and weighted using Bayesian parameter estimation. The resulting posterior parameter distribution describes a statistical ensemble of parameter sets; the parameter variances and correlations can account for missing knowledge, measurement

Dependence of radiocaesium biological half-life in freshwater fish on water potassium concentration and temperature

International Nuclear Information System (INIS)

Carreiro, M.C.V.; Corisco, J.A.G.

1998-01-01

Short-term experiments (35-49 days) showed that the rate of cesium elimination from fish increases with increasing potassium concentration in water (the biological half-life decreases); this, however, is only true of the potassium concentration range of 0.35 to 3.5 ppm, whereas higher potassium concentrations do not seem to affect the elimination rate. Decrease in water temperature within the 20 degC to 5 degC range slows down the cesium elimination process. (P.A.)

Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine.

Science.gov (United States)

Zhang, Xi

2017-02-01

Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Region and cell-type resolved quantitative proteomic map of the human heart

DEFF Research Database (Denmark)

Doll, Sophia; Dreßen, Martina; Geyer, Philipp E

2017-01-01

The heart is a central human organ and its diseases are the leading cause of death worldwide, but an in-depth knowledge of the identity and quantity of its constituent proteins is still lacking. Here, we determine the healthy human heart proteome by measuring 16 anatomical regions and three major...... cardiac cell types by high-resolution mass spectrometry-based proteomics. From low microgram sample amounts, we quantify over 10,700 proteins in this high dynamic range tissue. We combine copy numbers per cell with protein organellar assignments to build a model of the heart proteome at the subcellular...

Half-lives for selected actinides and long-lived radionuclides

International Nuclear Information System (INIS)

Holden, N.E.

1988-01-01

Long-lived actinide nuclides are of interest for their use in nuclear reactors, for nuclear reactor burnup studies in waste management, and for safeguard applications, e.g., α counting is used to determine the amount of material present. Some long-lived radionuclides are of interest for their use in determining geological ages using various dating methods, and in calculating the cosmic-ray exposure ages of meteorites. Recommended values are presented for both the total half-life and for the spontaneous fission half-life of /sup 232-236,238/U, of /sup 236,238-242,244/Pu, of /sup 241,242m,243/Am, and of /sup 242-248,250/Cm. Problems with the presentation of uncertainties are discussed. The impact of the revised 14 C half-life on the carbon dating technique and various 14 C ages is discussed. The possible primordial occurrence of 92 Nb is now definitely ruled out. Based on examination of the 26 Al half-life, the calculated value for the cosmic-ray exposure age of meteorites remains too high compared to the age calculated using other radionuclide half-life values. 204 Pb, which was once thought to be radioactive, is shown to be stable. 37 refs., 5 tabs

Proteomic analysis of Bombyx mori molting fluid: Insights into the molting process.

Science.gov (United States)

Liu, Hua-Wei; Wang, Luo-Ling; Tang, Xin; Dong, Zhao-Ming; Guo, Peng-Chao; Zhao, Dong-Chao; Xia, Qing-You; Zhao, Ping

2018-02-20

Molting is an essential biological process occurring multiple times throughout the life cycle of most Ecdysozoa. Molting fluids accumulate and function in the exuvial space during the molting process. In this study, we used liquid chromatography-tandem mass spectrometry to investigate the molting fluids to analyze the molecular mechanisms of molting in the silkworm, Bombyx mori. In total, 375 proteins were identified in molting fluids from the silkworm at 14-16h before pupation and eclosion, including 12 chitin metabolism-related enzymes, 35 serine proteases, 15 peptidases, and 38 protease inhibitors. Gene ontology analysis indicated that "catalytic" constitutes the most enriched function in the molting fluid. Gene expression patterns and bioinformatic analyses suggested that numerous enzymes are involved in the degradation of cuticle proteins and chitin. Protein-protein interaction network and activity analyses showed that protease inhibitors are involved in the regulation of multiple pathways in molting fluid. Additionally, many immune-related proteins may be involved in the immune defense during molting. These results provide a comprehensive proteomic insight into proteolytic enzymes and protease inhibitors in molting fluid, and will likely improve the current understanding of physiological processes in insect molting. Insect molting constitutes a dynamic physiological process. To better understand this process, we used LC-MS/MS to investigate the proteome of silkworm molting fluids and identified key proteins involved in silkworm molting. The biological processes of the old cuticle degradation pathway and immune defense response were analyzed in the proteome of silkworm molting fluid. We report that protease inhibitors serve as key factors in the regulation of the molting process. The proteomic results provide new insight into biological molting processes in insects. Copyright © 2017 Elsevier B.V. All rights reserved.

Platelet half-life in patients with primary hyperlipoproteinemia type IIa, IIb, and IV according to Fredrickson with and without clinical signs of atherosclerosis

Energy Technology Data Exchange (ETDEWEB)

Jaeger, E; Sinzinger, H; Widhalm, K; Kaliman, J; Hoefer, R [Vienna Univ. (Austria). 2. Medizinische Klinik; Ludwig Boltzmann-Institut fuer Nuklearmedizin, Vienna (Austria); Vienna Univ. (Austria). Kinderklinik; Vienna Univ. (Austria). Kardiologische Klinik)

1982-09-01

It is generally accepted that platelet half-life is shortened in atherosclerotic vascular diseases. Concerning changes due to hyperlipoproteinemia (HLP), however, there exist only few data. Therefore, we examined the platelet-half life in 60 patients with recently discovered HLP type IIa, IIb and IV according to Fredrickson before treatment in comparison to 60 controls. 33 of the HLP-patients had no clinical symptoms of angiopathy. 27 patients suffered from peripheral vascular disease or from coronary heart disease as verified by angiography. The labelling of autologous platelets was performed with 100..mu..Ci of /sup 111/Indium-oxine-sulfate at 37/sup 0/C for 5 minutes. The mean labelling efficiency was 90%, the recovery after 2 hours about 70%. Serum lipoproteins were estimated by means of ultracentrifugation and polyanionprecipitation according to Lipid Research Clinic Methods. In the patients with HLP platelet half-life was significantly shortened in comparison to the control group (p < 0.01). These changes were most pronounced in patients with HLP-type IIa and with atherosclerotic lesions, respectively. In patients with HLP-type IIa a very close correlation could be demonstrated between platelet half-life and LDL-cholesterol (r = -0.72; p < 0.001) as well as total cholesterol (r = -0.73; p < 0.001). These data prove that in HLP in-vivo platelet function as measured by platelet survival is significantly influenced even before the occurrence of clinically relevant symptoms of atherosclerosis.

Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

Directory of Open Access Journals (Sweden)

Tue Bjerg Bennike

2015-12-01

In addition, we analyzed the proteome of human plasma, and compared the proteomes to the obtained porcine synovial fluid proteome. The proteome of the two body fluids were found highly similar, underlining the detected plasma derived nature of many synovial fluid components. The healthy porcine synovial fluid proteomics data, human rheumatoid arthritis synovial fluid proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935.

ProteomicsDB.

Science.gov (United States)

Schmidt, Tobias; Samaras, Patroklos; Frejno, Martin; Gessulat, Siegfried; Barnert, Maximilian; Kienegger, Harald; Krcmar, Helmut; Schlegl, Judith; Ehrlich, Hans-Christian; Aiche, Stephan; Kuster, Bernhard; Wilhelm, Mathias

2018-01-04

ProteomicsDB (https://www.ProteomicsDB.org) is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of the human proteome. To date, it contains quantitative data from 78 projects totalling over 19k LC-MS/MS experiments. A standardized analysis pipeline enables comparisons between multiple datasets to facilitate the exploration of protein expression across hundreds of tissues, body fluids and cell lines. We recently extended the data model to enable the storage and integrated visualization of other quantitative omics data. This includes transcriptomics data from e.g. NCBI GEO, protein-protein interaction information from STRING, functional annotations from KEGG, drug-sensitivity/selectivity data from several public sources and reference mass spectra from the ProteomeTools project. The extended functionality transforms ProteomicsDB into a multi-purpose resource connecting quantification and meta-data for each protein. The rich user interface helps researchers to navigate all data sources in either a protein-centric or multi-protein-centric manner. Several options are available to download data manually, while our application programming interface enables accessing quantitative data systematically. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Determination of short half-life elements in biological, foodstuff, and environmental samples qualitatively by neutron activation analysis

International Nuclear Information System (INIS)

Syukria Kurniawati; Muhayatun Santoso; Diah Dwiana Lestiani

2010-01-01

NAA applications at routine operation power of 15 MW at Multipurpose Reactor GA Siwabessy (MPR-GAS) for sample matrices analysis have been widely applied. However, the results are not optimum for some matrices especially for short half-live elements. Preliminary study of short half-life elements determination in biological, foodstuff, and environmental samples using 1 MW power have been conducted to solve this problem. The samples were irradiated in rabbit system of MPR-GAS for 5 minutes, counted for 200 seconds by HPGe detector, and the spectrum were analyzed further using software Genie 2000 and Bandung NAA Utility. Analysis under 1 MW power on biological and foodstuff samples were capable to detect eight elements: Al, Br, CI, Ca, I, K, Mg, Ti, and Na for biological samples; Al, Br, CI, Ca, I, K, Mg, Mn, and Na for foodstuff samples, while at 15 MW power only three elements (CI, K, Na) were detected. At 1 MW power the counting process is more optimum due to smaller radiation exposure and dead time. For the environmental samples, the number of elements detected by 1 MW and 15 MW powers did not differ significantly. Generally, the results on the three types of samples showed that the elements of short half-life are better detected at 1 MW than that of 15 MW power. Further research needs to be done to obtain the optimum analytical conditions for irradiation and counting time determination. (author)

Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis.

Science.gov (United States)

Finka, Andrija; Goloubinoff, Pierre

2013-09-01

In the crowded environment of human cells, folding of nascent polypeptides and refolding of stress-unfolded proteins is error prone. Accumulation of cytotoxic misfolded and aggregated species may cause cell death, tissue loss, degenerative conformational diseases, and aging. Nevertheless, young cells effectively express a network of molecular chaperones and folding enzymes, termed here "the chaperome," which can prevent formation of potentially harmful misfolded protein conformers and use the energy of adenosine triphosphate (ATP) to rehabilitate already formed toxic aggregates into native functional proteins. In an attempt to extend knowledge of chaperome mechanisms in cellular proteostasis, we performed a meta-analysis of human chaperome using high-throughput proteomic data from 11 immortalized human cell lines. Chaperome polypeptides were about 10% of total protein mass of human cells, half of which were Hsp90s and Hsp70s. Knowledge of cellular concentrations and ratios among chaperome polypeptides provided a novel basis to understand mechanisms by which the Hsp60, Hsp70, Hsp90, and small heat shock proteins (HSPs), in collaboration with cochaperones and folding enzymes, assist de novo protein folding, import polypeptides into organelles, unfold stress-destabilized toxic conformers, and control the conformal activity of native proteins in the crowded environment of the cell. Proteomic data also provided means to distinguish between stable components of chaperone core machineries and dynamic regulatory cochaperones.

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver.

Science.gov (United States)

Mauvoisin, Daniel; Wang, Jingkui; Jouffe, Céline; Martin, Eva; Atger, Florian; Waridel, Patrice; Quadroni, Manfredo; Gachon, Frédéric; Naef, Felix

2014-01-07

Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known about the accumulation patterns of proteins. Here, we quantified temporal profiles in the murine hepatic proteome under physiological light-dark conditions using stable isotope labeling by amino acids quantitative MS. Our analysis identified over 5,000 proteins, of which several hundred showed robust diurnal oscillations with peak phases enriched in the morning and during the night and related to core hepatic physiological functions. Combined mathematical modeling of temporal protein and mRNA profiles indicated that proteins accumulate with reduced amplitudes and significant delays, consistent with protein half-life data. Moreover, a group comprising about one-half of the rhythmic proteins showed no corresponding rhythmic mRNAs, indicating significant translational or posttranslational diurnal control. Such rhythms were highly enriched in secreted proteins accumulating tightly during the night. Also, these rhythms persisted in clock-deficient animals subjected to rhythmic feeding, suggesting that food-related entrainment signals influence rhythms in circulating plasma factors.

Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection.

Science.gov (United States)

Kulej, Katarzyna; Avgousti, Daphne C; Sidoli, Simone; Herrmann, Christin; Della Fera, Ashley N; Kim, Eui Tae; Garcia, Benjamin A; Weitzman, Matthew D

2017-04-01

Herpes simplex virus (HSV-1) lytic infection results in global changes to the host cell proteome and the proteins associated with host chromatin. We present a system level characterization of proteome dynamics during infection by performing a multi-dimensional analysis during HSV-1 lytic infection of human foreskin fibroblast (HFF) cells. Our study includes identification and quantification of the host and viral proteomes, phosphoproteomes, chromatin bound proteomes and post-translational modifications (PTMs) on cellular histones during infection. We analyzed proteomes across six time points of virus infection (0, 3, 6, 9, 12 and 15 h post-infection) and clustered trends in abundance using fuzzy c-means. Globally, we accurately quantified more than 4000 proteins, 200 differently modified histone peptides and 9000 phosphorylation sites on cellular proteins. In addition, we identified 67 viral proteins and quantified 571 phosphorylation events (465 with high confidence site localization) on viral proteins, which is currently the most comprehensive map of HSV-1 phosphoproteome. We investigated chromatin bound proteins by proteomic analysis of the high-salt chromatin fraction and identified 510 proteins that were significantly different in abundance during infection. We found 53 histone marks significantly regulated during virus infection, including a steady increase of histone H3 acetylation (H3K9ac and H3K14ac). Our data provide a resource of unprecedented depth for human and viral proteome dynamics during infection. Collectively, our results indicate that the proteome composition of the chromatin of HFF cells is highly affected during HSV-1 infection, and that phosphorylation events are abundant on viral proteins. We propose that our epi-proteomics approach will prove to be important in the characterization of other model infectious systems that involve changes to chromatin composition. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Phenobarbital administration every eight hours: improvement of seizure management in idiopathic epileptic dogs with decreased phenobarbital elimination half-life.

Science.gov (United States)

Stabile, F; Barnett, C R; De Risio, L

2017-02-18

Estimated prevalence of canine idiopathic epilepsy is 0.6 per cent in the first-opinion canine population in the UK. Phenobarbital monotherapy has been reported to reduce/eradicate seizure activity in 60-93 per cent of idiopathic epileptic dogs (IEDs). The objective of this study was to evaluate safety and efficacy of the administration of phenobarbital orally every eight hours in IEDs with phenobarbital elimination half-life less than 20 hours. Medical records of 10 IEDs in which steady state trough serum phenobarbital levels were within the reference range and phenobarbital elimination half-life had become less than 20 hours following prolonged administration every 12 hours were reviewed. Side effects and seizure frequency when phenobarbital was administered every 12 hours or 8 hours were compared. In all dogs the side effects of the antiepileptic medication treatment improved. When phenobarbital was administered every eight hours, 9/10 dogs experienced improvement in seizure frequency and 8/10 dogs maintained seizure freedom for a period three times longer than the longest interictal interval period previously recorded. Reduction in the severity and number of clusters of seizures was recorded in one of the remaining two dogs. The administration of phenobarbital orally every eight hours in IEDs with decreased phenobarbital elimination half-life appears safe and can improve seizure management. The results of this study were presented in abstract form (poster) for the 28th symposium of the European Society of Veterinary Neurology - European College of Veterinary Neurology (ESVN), September 18-19, 2015, Amsterdam, Netherlands. British Veterinary Association.

Clinical veterinary proteomics: Techniques and approaches to decipher the animal plasma proteome.

Science.gov (United States)

Ghodasara, P; Sadowski, P; Satake, N; Kopp, S; Mills, P C

2017-12-01

Over the last two decades, technological advancements in the field of proteomics have advanced our understanding of the complex biological systems of living organisms. Techniques based on mass spectrometry (MS) have emerged as powerful tools to contextualise existing genomic information and to create quantitative protein profiles from plasma, tissues or cell lines of various species. Proteomic approaches have been used increasingly in veterinary science to investigate biological processes responsible for growth, reproduction and pathological events. However, the adoption of proteomic approaches by veterinary investigators lags behind that of researchers in the human medical field. Furthermore, in contrast to human proteomics studies, interpretation of veterinary proteomic data is difficult due to the limited protein databases available for many animal species. This review article examines the current use of advanced proteomics techniques for evaluation of animal health and welfare and covers the current status of clinical veterinary proteomics research, including successful protein identification and data interpretation studies. It includes a description of an emerging tool, sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS), available on selected mass spectrometry instruments. This newly developed data acquisition technique combines advantages of discovery and targeted proteomics approaches, and thus has the potential to advance the veterinary proteomics field by enhancing identification and reproducibility of proteomics data. Copyright © 2017 Elsevier Ltd. All rights reserved.

Positional proteomics in the era of the human proteome project on the doorstep of precision medicine.

Science.gov (United States)

Eckhard, Ulrich; Marino, Giada; Butler, Georgina S; Overall, Christopher M

2016-03-01

Proteolytic processing is a pervasive and irreversible post-translational modification that expands the protein universe by generating new proteoforms (protein isoforms). Unlike signal peptide or prodomain removal, protease-generated proteoforms can rarely be predicted from gene sequences. Positional proteomic techniques that enrich for N- or C-terminal peptides from proteomes are indispensable for a comprehensive understanding of a protein's function in biological environments since protease cleavage frequently results in altered protein activity and localization. Proteases often process other proteases and protease inhibitors which perturbs proteolytic networks and potentiates the initial cleavage event to affect other molecular networks and cellular processes in physiological and pathological conditions. This review is aimed at researchers with a keen interest in state of the art systems level positional proteomic approaches that: (i) enable the study of complex protease-protease, protease-inhibitor and protease-substrate crosstalk and networks; (ii) allow the identification of proteolytic signatures as candidate disease biomarkers; and (iii) are expected to fill the Human Proteome Project missing proteins gap. We predict that these methodologies will be an integral part of emerging precision medicine initiatives that aim to customize healthcare, converting reactive medicine into a personalized and proactive approach, improving clinical care and maximizing patient health and wellbeing, while decreasing health costs by eliminating ineffective therapies, trial-and-error prescribing, and adverse drug effects. Such initiatives require quantitative and functional proteome profiling and dynamic disease biomarkers in addition to current pharmacogenomics approaches. With proteases at the pathogenic center of many diseases, high-throughput protein termini identification techniques such as TAILS (Terminal Amine Isotopic Labeling of Substrates) and COFRADIC (COmbined

Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

Science.gov (United States)

Schaab, Christoph; Geiger, Tamar; Stoehr, Gabriele; Cox, Juergen; Mann, Matthias

2012-03-01

MS-based proteomics generates rapidly increasing amounts of precise and quantitative information. Analysis of individual proteomic experiments has made great strides, but the crucial ability to compare and store information across different proteome measurements still presents many challenges. For example, it has been difficult to avoid contamination of databases with low quality peptide identifications, to control for the inflation in false positive identifications when combining data sets, and to integrate quantitative data. Although, for example, the contamination with low quality identifications has been addressed by joint analysis of deposited raw data in some public repositories, we reasoned that there should be a role for a database specifically designed for high resolution and quantitative data. Here we describe a novel database termed MaxQB that stores and displays collections of large proteomics projects and allows joint analysis and comparison. We demonstrate the analysis tools of MaxQB using proteome data of 11 different human cell lines and 28 mouse tissues. The database-wide false discovery rate is controlled by adjusting the project specific cutoff scores for the combined data sets. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted. We used MaxQB to calculate the signal reproducibility of the detected peptides for the same proteins across different proteomes. Spearman rank correlation between peptide intensity and detection probability of identified proteins was greater than 0.8 for 64% of the proteome, whereas a minority of proteins have negative correlation. This information can be used to pinpoint false protein identifications, independently of peptide database

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

DEFF Research Database (Denmark)

Yang, Laurence; Tan, Justin; O'Brien, Edward J.

2015-01-01

based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma......Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood...... at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass...

Dynamics of the proteome in human and farm animal milk

NARCIS (Netherlands)

Zhang, L.

2015-01-01

Abstract

The milk proteome changes due to many factors, such as lactation, individual, health status, processing, and species differences. The objective of the work described in this thesis was to increase our

Mass spectrometry analysis of proteome-wide proteolytic post-translational degradation of proteins

OpenAIRE

Shen, Yufeng; Hixson, Kim K.; Tolić, Nikola; Camp, David G.; Purvine, Samuel O.; Moore, Ronald J.; Smith, Richard D.

2008-01-01

Protein proteolytic degradation is an essential component to proper cell function and its life cycle. Here, we study the protein degradation in yeast Saccharomyces cerevisiae cells on a proteome-wide scale by detection of the intermediate peptides produced from the intracellular degradation of proteins using sequencing-based tandem mass spectrometry. By tracing the detected ~1,100 peptides and their ~200 protein substrate origins we obtain evidence for new insights into the proteome-wide prot...

Small business life cycle: statics and dynamics (S

Directory of Open Access Journals (Sweden)

Matejun Marek

2017-12-01

Full Text Available The aim of the paper is the presentation of theoretical foundations and the structure of original, 8-stage statics and dynamics model in the small business life cycle. Based on theoretical considerations, two hypotheses concerning the impact of dynamic and static nature of the life-cycle stages on selected determinants and effects of SMEs’ development were formulated. The hypotheses were verified based on the results of the survey conducted on a sample of 1,741 SMEs from 22 countries of the European Union. The results indicate that companies in the dynamic life-cycle stages are run by more enterprising owners, operate in more promising markets with a higher potential and make greater use of market niches thus limiting the level of competition. At the same time, such companies are characterised by higher levels of flexibility and involvement in innovative activities, which translates into obtaining a significantly higher level of business performance, in the area of quantitative as well as qualitative results.

Biological Half-Life Measurements of Radioactive Strontium in Hormonal-Resistant Prostate Cancer Patients

International Nuclear Information System (INIS)

Haquin, G.; Riemer, T.; Kaniun, N.; Datz, H.; Yungreiss, Z.; Vexler, A.; Ben-Yosef, R.; Pelled, O.; German, U.; Marko, R.; Teshuva, A.; Kol, R.

2004-01-01

Therapy for metastatic bone pain in Hormonal-Resistant Prostate Cancer (HRPC) patients is performed by administering systemic radioisotope therapy [1]. The beta radiation emitted by the radioactive strontium 89 Sr [T 1/2 =50.5 d, E β (max)=1.49 MeV], an adequate radionuclide for this therapy procedure, irradiates the metastatic cells in the bone, producing the desired palliative effect. The beta disintegration of 89 Sr is followed by a low abundance (0.00945%) gamma ray with energy of 909 keV. The commercially available 89 Sr is in the form of Sr Cl and contains an impurity of less than 0.5% of 85 Sr [T 1/2 =64.8 d] ,which decays by electron capture, emitting gamma rays at 511 keV (95.71%). The radiation dose to the metastatic cells due to the gamma rays is negligible compared to the dose given by the beta radiation, assuming that the 89 Sr is concentrated at the metastatic bony lesions. Accurate information about retention and excretion of Sr in the patient's body will contribute to better evaluate the effectiveness of the treatment. he effective half-life of 89 Sr can be calculated either from Whole Body Counting (WBC) measurements or by measuring 85 Sr and/or 89 Sr in urine/blood. WBC measurements, using collimated HPGe detectors, allow the follow-up of 89 Sr and 85 Sr at different sites in the skeletal bones of the patient. Biological half-lives of Sr in different body sections measured by WBC and the correlation with excretion-rate-based biological half-lives are presented

High-throughput proteomics : optical approaches.

Energy Technology Data Exchange (ETDEWEB)

Davidson, George S.

2008-09-01

Realistic cell models could greatly accelerate our ability to engineer biochemical pathways and the production of valuable organic products, which would be of great use in the development of biofuels, pharmaceuticals, and the crops for the next green revolution. However, this level of engineering will require a great deal more knowledge about the mechanisms of life than is currently available. In particular, we need to understand the interactome (which proteins interact) as it is situated in the three dimensional geometry of the cell (i.e., a situated interactome), and the regulation/dynamics of these interactions. Methods for optical proteomics have become available that allow the monitoring and even disruption/control of interacting proteins in living cells. Here, a range of these methods is reviewed with respect to their role in elucidating the interactome and the relevant spatial localizations. Development of these technologies and their integration into the core competencies of research organizations can position whole institutions and teams of researchers to lead in both the fundamental science and the engineering applications of cellular biology. That leadership could be particularly important with respect to problems of national urgency centered around security, biofuels, and healthcare.

A critical oscillation constant as a variable of time scales for half-linear dynamic equations

Czech Academy of Sciences Publication Activity Database

Řehák, Pavel

2010-01-01

Roč. 60, č. 2 (2010), s. 237-256 ISSN 0139-9918 R&D Projects: GA AV ČR KJB100190701 Institutional research plan: CEZ:AV0Z10190503 Keywords : dynamic equation * time scale * half-linear equation * (non)oscillation criteria * Hille-Nehari criteria * Kneser criteria * critical constant * oscillation constant * Hardy inequality Subject RIV: BA - General Mathematics Impact factor: 0.316, year: 2010 http://link.springer.com/article/10.2478%2Fs12175-010-0009-7

Direct Deposition Effect on the Distribution of Radiocesium in Persimmon Trees and the Effective Half-life

Energy Technology Data Exchange (ETDEWEB)

Tagami, Keiko; Uchida, Shigeo [National Institute of Radiological Sciences, Anagawa 4-9-1, Inage-ku, Chiba 263-7444 (Japan)

2014-07-01

Radiocesium ({sup 137}Cs) concentrations in persimmon tree tissues collected at Chiba, about 220 km south from Fukushima Daiichi nuclear power plant (FDNPP), were measured to obtain half-life of radiocesium in the trees. Persimmon (Diospyros kaki) is a deciduous tree and bears edible fruits in autumn. There were no leaves when the sampling area was received the radioactive fallout in March 2011 due to the FDNPP accident; the amount of {sup 137}Cs radioactivity in this area was ca. 13 kBq/m{sup 3} Both {sup 137}Cs and {sup 134}Cs were found in the newly emerged shoots of the persimmon trees collected at 26 April 2011 mainly due to foliar uptake. The concentrations were 1.1 kBq/kg-dry for {sup 137}Cs and 1.3 kBq/kg-dry for {sup 134}Cs. After that, continuous sampling of leaves, branches and fruits of the persimmon trees had been carried out for two years. Immediately after the collection, samples were transferred to our laboratory and weighed to obtain fresh weight. Leaf samples were usually separated into two portions; one portion was washed with tap water to remove dust from the surface and the other portion was not treated. For fruit samples, if it is possible, fruit flesh, peal and non-edible part were separated. All the samples were oven-dried at 80 deg. C for three days at least. Each dried sample was chopped into fine pieces, mixed well, and then transferred into plastic vessels separately. Radioactivity concentration was measured by a Ge-detecting system (Seiko EG and G Ortec) using 3000-40000 s counting intervals. By August 14, 2013, about 140 samples were collected from the trees; about 60 samples were leaves (both washed and untreated). Radiocesium concentrations in tree leaves decreased with time, and the effective half-life was about 190 d; the value was similar to those in branches (160 d for new branches, and 250 d for 1-2 y.o. branches) and fruits (250 d for fruit flesh and 230 d for peals). Thus we concluded that the half-life of radiocesium in

Measuring radioactive half-lives via statistical sampling in practice

Science.gov (United States)

Lorusso, G.; Collins, S. M.; Jagan, K.; Hitt, G. W.; Sadek, A. M.; Aitken-Smith, P. M.; Bridi, D.; Keightley, J. D.

2017-10-01

The statistical sampling method for the measurement of radioactive decay half-lives exhibits intriguing features such as that the half-life is approximately the median of a distribution closely resembling a Cauchy distribution. Whilst initial theoretical considerations suggested that in certain cases the method could have significant advantages, accurate measurements by statistical sampling have proven difficult, for they require an exercise in non-standard statistical analysis. As a consequence, no half-life measurement using this method has yet been reported and no comparison with traditional methods has ever been made. We used a Monte Carlo approach to address these analysis difficulties, and present the first experimental measurement of a radioisotope half-life (211Pb) by statistical sampling in good agreement with the literature recommended value. Our work also focused on the comparison between statistical sampling and exponential regression analysis, and concluded that exponential regression achieves generally the highest accuracy.

Proteomics dataset

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

2017-01-01

The datasets presented in this article are related to the research articles entitled “Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies” (Bennike et al., 2015 [1]), and “Proteome Analysis of Rheumatoid Arthritis Gut Mucosa” (Bennike et al., 2017 [2])...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

How cyclophosphamide at environmentally relevant concentration influences Daphnia magna life history and its proteome.

Directory of Open Access Journals (Sweden)

Małgorzata Grzesiuk

Full Text Available The waste of commonly used medicines is known to contaminate freshwater ecosystems. Pharmaceuticals can be toxic, mutagenic, or modifying to freshwater organisms even at low concentrations if consider their permanent presence in the environment. Chemotherapeutics used to treat cancer, and in particular alkylating agents, contribute significantly to this form of pollution, the latter introducing cytotoxic and/or mutagenic lesions to the DNA and RNA of organisms which can be disruptive to their cells. The aim of the present study was to investigate the influence of the alkylating anticancer agent cyclophosphamide (CP on Daphnia magna clones. We evaluated the life history parameters and protein profiles of this crustacean following exposure to environmentally relevant CP concentration of 10 ng L-1. Even at this low concentration, the alkylating agent caused modification of the life history parameters and proteome profile of the Daphnia. These changes were clone-specific and involved growth rate, age at first reproduction, neonate number, and proteins related to cell cycle and redox state regulation. The disturbance caused by pharmaceuticals contaminating freshwater ecosystem is probably weaker and unlikely to be cytotoxic in character due to the high dilution of these substances in the water. However, our results indicate that prolonged exposure of organisms to these toxins may lead to modifications on the organismal and molecular levels with unpredictable significance for the entire ecosystem.

Determination of the half-life of sup 1 sup 0 sup 5 sup m Rh

CERN Document Server

Kronenberg, A K; Weber, R; Esterlund, R A; Patzelt, P

1998-01-01

Following a fast chemical separation of Ru isotopes from a fission-product mixture, sup 1 sup 0 sup 5 sup m Rh was periodically extracted from its precursor (4.44-h sup 1 sup 0 sup 5 Ru) for measurements of its half-life. The new value for the T sub 1 sub / sub 2 of sup 1 sup 0 sup 5 sup m Rh of (43.0+-0.3) s resolves the long-standing conflict in the literature between the two earlier measured values of 45 and 30 s.

Social network architecture of human immune cells unveiled by quantitative proteomics.

Science.gov (United States)

Rieckmann, Jan C; Geiger, Roger; Hornburg, Daniel; Wolf, Tobias; Kveler, Ksenya; Jarrossay, David; Sallusto, Federica; Shen-Orr, Shai S; Lanzavecchia, Antonio; Mann, Matthias; Meissner, Felix

2017-05-01

The immune system is unique in its dynamic interplay between numerous cell types. However, a system-wide view of how immune cells communicate to protect against disease has not yet been established. We applied high-resolution mass-spectrometry-based proteomics to characterize 28 primary human hematopoietic cell populations in steady and activated states at a depth of >10,000 proteins in total. Protein copy numbers revealed a specialization of immune cells for ligand and receptor expression, thereby connecting distinct immune functions. By integrating total and secreted proteomes, we discovered fundamental intercellular communication structures and previously unknown connections between cell types. Our publicly accessible (http://www.immprot.org/) proteomic resource provides a framework for the orchestration of cellular interplay and a reference for altered communication associated with pathology.

Proteomics research in India: an update.

Science.gov (United States)

Reddy, Panga Jaipal; Atak, Apurva; Ghantasala, Saicharan; Kumar, Saurabh; Gupta, Shabarni; Prasad, T S Keshava; Zingde, Surekha M; Srivastava, Sanjeeva

2015-09-08

After a successful completion of the Human Genome Project, deciphering the mystery surrounding the human proteome posed a major challenge. Despite not being largely involved in the Human Genome Project, the Indian scientific community contributed towards proteomic research along with the global community. Currently, more than 76 research/academic institutes and nearly 145 research labs are involved in core proteomic research across India. The Indian researchers have been major contributors in drafting the "human proteome map" along with international efforts. In addition to this, virtual proteomics labs, proteomics courses and remote triggered proteomics labs have helped to overcome the limitations of proteomics education posed due to expensive lab infrastructure. The establishment of Proteomics Society, India (PSI) has created a platform for the Indian proteomic researchers to share ideas, research collaborations and conduct annual conferences and workshops. Indian proteomic research is really moving forward with the global proteomics community in a quest to solve the mysteries of proteomics. A draft map of the human proteome enhances the enthusiasm among intellectuals to promote proteomic research in India to the world.This article is part of a Special Issue entitled: Proteomics in India. Copyright © 2015 Elsevier B.V. All rights reserved.

Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

Directory of Open Access Journals (Sweden)

Sarah Lück

2014-10-01

Full Text Available The rich mammalian cellular circadian output affects thousands of genes in many cell types and has been the subject of genome-wide transcriptome and proteome studies. The results have been enigmatic because transcript peak abundances do not always follow the peaks of gene-expression activity in time. We posited that circadian degradation of mRNAs and proteins plays a pivotal role in setting their peak times. To establish guiding principles, we derived a theoretical framework that fully describes the amplitudes and phases of biomolecules with circadian half-lives. We were able to explain the circadian transcriptome and proteome studies with the same unifying theory, including cases in which transcripts or proteins appeared before the onset of increased production rates. Furthermore, we estimate that 30% of the circadian transcripts in mouse liver and Drosophila heads are affected by rhythmic posttranscriptional regulation.

[Diet and exercise influence on the proteomic profile of an athlete population].

Science.gov (United States)

Toro, Rocio; Mangas, Alipio; Quezada, Maribel; Rodriguez-Rosety, Manuel; Fournielles, Gabriel; Rodriguez-Rosety, Ignacio; Rodriguez Rosety, Miguel Angel; Alonso, Jose Angel; Garcia-Cozar, Francisco Jose; Duran, Maria Del Carmen

2014-11-01

Nutrition has emerged as a fundamental tool included in the training program of athletes. Body composition seeks different objectives depending on type of sport, position, or time of the season. Furthermore, analysis proteomics allows us to know the structure and function of proteins. To study, using proteomics, the influence of two different diets on the anthropometric profile in a rugby players group. It is a prospective and interventionist study. Thirty-two rugby players were included. Two groups were defined, one followed proteic diet (PD) and, the other group subscribed the Mediterranean diet (MD). All participants were evaluated anthropometrically at the beginning and after six months. A blood sample was taken to twenty -two players, half of each group, used for the proteomic analysis. MD highlight more benefit for these athletes. Two groups were defined based on their anthropometric behavior, G1 and G2. The proteomic analysis related significantly some TGF-family mediators with these groups. MD improves the muscular mass without increasing the total body weight, so this data could be determinant to define profiles for athletes. Some TGF-members could be implicated in the adipose tissue and muscular mass balance. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Dynamics of vortices in polariton quantum fluids : From full vortices, to half vortices and vortex pairs

Science.gov (United States)

Deveaud-Plédran, Benoit

2012-02-01

Polariton quantum fluids may be created both spontaneously through a standard phase transition towards a Bose Einstein condensate, or may be resonantly driven with a well-defined speed. Thanks to the photonic component of polaritons, the properties of the quantum fluid may be accessed rather directly with in particular the possibility of detained interferometric studies. Here, I will detail the dynamics of vortices, obtained with a picosecond time resolution, in different configurations, with in particular their phase dynamics. I will show in particular the dynamics the dynamics of spontaneous creation of a vortex, the dissociation of a full vortex into two half vortices as well as the dynamics of the dissociation of a dark soliton line into a street of pairs of vortices. Work done at EPFL by a dream team of Postdocs PhD students and collaborators: K. Lagoudakis, G. Nardin, T. Paraiso, G. Grosso, F. Manni, Y L'eger, M. Portella Oberli, F. Morier-Genoud and the help of our friend theorists V, Savona, M. Vouters and T. Liew.

Comparative Proteome and Phosphoproteome Analyses during Cyprid Development of the Barnacle Balanus ( =Amphibalanus ) amphitrite

KAUST Repository

Zhang, Yu

2010-06-04

The barnacle Balanus amphitrite (=Amphibalanus amphitrite) is a major marine biofouling invertebrate worldwide. It has a complex life cycle during which the larva (called a nauplius) molts six times before transforming into the cyprid stage. The cyprid stage in B. amphitrite is the critical stage for the larval decision to attach and metamorphose. In this study, proteome and phosphoproteome alterations during cyprid development/aging and upon treatment with the antifouling agent butenolide were examined with a two-dimensional electrophoresis (2-DE) multiplexed fluorescent staining approach. Optimized protein separation strategies, including solution-phase isoelectric fractionation and narrow-pH-range 2-DE, were used in a proteomic analysis. Our results show that the differential regulation of the target proteins is highly dynamic on the levels of both protein expression and posttranslational modification. Two groups of proteins, stress-associated and energy metabolism-related proteins, are differentially expressed during cyprid development. Comparison of the control and treatment groups suggests that butenolide exerts its effects by sustaining the expression levels of these proteins. Altogether, our data suggest that proteins involved in stress regulation and energy metabolism play crucial roles in regulating larval attachment and metamorphosis of B. amphitrite. © 2010 American Chemical Society.

Recent 5-year Findings and Technological Advances in the Proteomic Study of HIV-associated Disorders.

Science.gov (United States)

Zhang, Lijun; Jia, Xiaofang; Jin, Jun-O; Lu, Hongzhou; Tan, Zhimi

2017-04-01

Human immunodeficiency virus-1 (HIV-1) mainly relies on host factors to complete its life cycle. Hence, it is very important to identify HIV-regulated host proteins. Proteomics is an excellent technique for this purpose because of its high throughput and sensitivity. In this review, we summarized current technological advances in proteomics, including general isobaric tags for relative and absolute quantitation (iTRAQ) and stable isotope labeling by amino acids in cell culture (SILAC), as well as subcellular proteomics and investigation of posttranslational modifications. Furthermore, we reviewed the applications of proteomics in the discovery of HIV-related diseases and HIV infection mechanisms. Proteins identified by proteomic studies might offer new avenues for the diagnosis and treatment of HIV infection and the related diseases. Copyright © 2017 The Authors. Production and hosting by Elsevier B.V. All rights reserved.

Least square method of estimation of ecological half-lives of radionuclides in sediments

International Nuclear Information System (INIS)

Ranade, A.K.; Pandey, M.; Datta, D.; Ravi, P.M.

2012-01-01

Long term behavior of radionuclides in the environment is an important issue for estimating probable radiological consequences and associated risks. It is also useful for evaluating potential use of contaminated areas and the possible effectiveness of remediation activities. The long term behavior is quantified by means of ecological half life, a parameter that aggregates all processes except radioactive decay which causes a decrease of activity in a specific medium. The process involved in ecological half life depends upon the environmental condition of the medium involved. A fitting model based on least square regression approach was used to evaluate the ecological half life. This least square method has to run several times to evaluate the number of ecological half lives present in the medium for the radionuclide. The case study data considered here is for 137 Cs in Mumbai Harbour Bay. The study shows the trend of 137 Cs over the years at a location in Mumbai Harbour Bay. First iteration model illustrate the ecological half life as 4.94 y and subsequently it passes through a number of runs for more number of ecological half-life present by goodness of fit test. The paper presents a methodology for evaluating ecological half life and exemplifies it with a case study of 137 Cs. (author)

The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

Directory of Open Access Journals (Sweden)

Li Zhang

Full Text Available Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

Mass Spectrometry Instrumentation in Proteomics

DEFF Research Database (Denmark)

Sprenger, Richard Remko; Roepstorff, Peter

2012-01-01

Mass spectrometry has evolved into a crucial technology for the field of proteomics, enabling the comprehensive study of proteins in biological systems. Innovative developments have yielded flexible and versatile mass spectrometric tools, including quadrupole time-of-flight, linear ion trap......, Orbitrap and ion mobility instruments. Together they offer various and complementary capabilities in terms of ionization, sensitivity, speed, resolution, mass accuracy, dynamic range and methods of fragmentation. Mass spectrometers can acquire qualitative and quantitative information on a large scale...

Biological half-life and distribution of radiocesium in a contaminated population of green treefrogs Hyla cinerea

International Nuclear Information System (INIS)

Dapson, R.W.; Kaplan, L.

1975-01-01

Radiocesium content of adult male green treefrogs Hyla cinerea from a contaminated habitat is adequately described by a log normal distribution with mean 2.277 log 10 pCi g -1 dry wt (189.2 pCi g -1 ) and variance of 0.031. There was significant negative correlation of body burden with body length and weight (p 2 = 0.10). Biological half-life of radiocesium in unfed, captive frogs held at 20 deg - 30 deg C averaged 30.1 d. (author)

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

Directory of Open Access Journals (Sweden)

Christopher T. Brown

2018-04-01

Full Text Available During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC, a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

Science.gov (United States)

Xiong, Weili; Olm, Matthew R.; Thomas, Brian C.; Baker, Robyn; Firek, Brian; Morowitz, Michael J.; Hettich, Robert L.

2018-01-01

ABSTRACT During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context. PMID:29636439

Uranium half-lives: a critical review

International Nuclear Information System (INIS)

Holden, N.E.

1981-01-01

The experimental data are evaluated and values for the spontaneous fission half-life of 238 U and the total half-lives for 232 U, 233 U, 234 U, 235 U, 236 U, and 238 U are recommended. Also the variation of the isotopic abundance of 234 U in nature and the error involved in the assumption of secular equilibrium between 234 U and 238 U in the determination of the specific activity of natural uranium samples are discussed. The recommended half-life values and 95% confidence limits are: 238 U spontaneous fission: 8.09 +- 0.26 x 10 15 years; 232 U total: 69.8 +- 1.0 years; 233 U total: 1.592 +- 0.002 x 10 5 years; 234 U total: 2.454 +- 0.006 x 10 5 years; 235 U total: 7.037 +- 0.011 x 10 8 years; 236 U total: 2.342 +- 0.003 x 10 7 years 238 U total: 4.468 +- 0.005 x 10 9 years

[Proteomics and transfusion medicine].

Science.gov (United States)

Lion, N; Prudent, M; Crettaz, D; Tissot, J-D

2011-04-01

The term "proteomics" covers tools and techniques that are used to analyze and characterize complex mixtures of proteins from various biological samples. In this short review, a typical proteomic approach, related to the study of particular and illustrative situation related to transfusion medicine is reported. This "case report" will allow the reader to be familiar with a practical proteomic approach of a real situation, and will permit to describe the tools that are usually used in proteomic labs, and, in a second part, to present various proteomic applications in transfusion medicine. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

High-precision measurement of the 19Ne half-life and implications for right-handed weak currents.

Science.gov (United States)

Triambak, S; Finlay, P; Sumithrarachchi, C S; Hackman, G; Ball, G C; Garrett, P E; Svensson, C E; Cross, D S; Garnsworthy, A B; Kshetri, R; Orce, J N; Pearson, M R; Tardiff, E R; Al-Falou, H; Austin, R A E; Churchman, R; Djongolov, M K; D'Entremont, R; Kierans, C; Milovanovic, L; O'Hagan, S; Reeve, S; Sjue, S K L; Williams, S J

2012-07-27

We report a precise determination of the (19)Ne half-life to be T(1/2)=17.262±0.007 s. This result disagrees with the most recent precision measurements and is important for placing bounds on predicted right-handed interactions that are absent in the current standard model. We are able to identify and disentangle two competing systematic effects that influence the accuracy of such measurements. Our findings prompt a reassessment of results from previous high-precision lifetime measurements that used similar equipment and methods.

High-Precision Measurement of the Ne19 Half-Life and Implications for Right-Handed Weak Currents

Science.gov (United States)

Triambak, S.; Finlay, P.; Sumithrarachchi, C. S.; Hackman, G.; Ball, G. C.; Garrett, P. E.; Svensson, C. E.; Cross, D. S.; Garnsworthy, A. B.; Kshetri, R.; Orce, J. N.; Pearson, M. R.; Tardiff, E. R.; Al-Falou, H.; Austin, R. A. E.; Churchman, R.; Djongolov, M. K.; D'Entremont, R.; Kierans, C.; Milovanovic, L.; O'Hagan, S.; Reeve, S.; Sjue, S. K. L.; Williams, S. J.

2012-07-01

We report a precise determination of the Ne19 half-life to be T1/2=17.262±0.007s. This result disagrees with the most recent precision measurements and is important for placing bounds on predicted right-handed interactions that are absent in the current standard model. We are able to identify and disentangle two competing systematic effects that influence the accuracy of such measurements. Our findings prompt a reassessment of results from previous high-precision lifetime measurements that used similar equipment and methods.

Comparison of Models for Ball Bearing Dynamic Capacity and Life

Science.gov (United States)

Gupta, Pradeep K.; Oswald, Fred B.; Zaretsky, Erwin V.

2015-01-01

Generalized formulations for dynamic capacity and life of ball bearings, based on the models introduced by Lundberg and Palmgren and Zaretsky, have been developed and implemented in the bearing dynamics computer code, ADORE. Unlike the original Lundberg-Palmgren dynamic capacity equation, where the elastic properties are part of the life constant, the generalized formulations permit variation of elastic properties of the interacting materials. The newly updated Lundberg-Palmgren model allows prediction of life as a function of elastic properties. For elastic properties similar to those of AISI 52100 bearing steel, both the original and updated Lundberg-Palmgren models provide identical results. A comparison between the Lundberg-Palmgren and the Zaretsky models shows that at relatively light loads the Zaretsky model predicts a much higher life than the Lundberg-Palmgren model. As the load increases, the Zaretsky model provides a much faster drop off in life. This is because the Zaretsky model is much more sensitive to load than the Lundberg-Palmgren model. The generalized implementation where all model parameters can be varied provides an effective tool for future model validation and enhancement in bearing life prediction capabilities.

The interaction between thermodynamic stability and buried free cysteines in regulating the functional half-life of fibroblast growth factor-1.

Science.gov (United States)

Lee, Jihun; Blaber, Michael

2009-10-16

Protein biopharmaceuticals are an important and growing area of human therapeutics; however, the intrinsic property of proteins to adopt alternative conformations (such as during protein unfolding and aggregation) presents numerous challenges, limiting their effective application as biopharmaceuticals. Using fibroblast growth factor-1 as model system, we describe a cooperative interaction between the intrinsic property of thermostability and the reactivity of buried free-cysteine residues that can substantially modulate protein functional half-life. A mutational strategy that combines elimination of buried free cysteines and secondary mutations that enhance thermostability to achieve a substantial gain in functional half-life is described. Furthermore, the implementation of this design strategy utilizing stabilizing mutations within the core region resulted in a mutant protein that is essentially indistinguishable from wild type as regard protein surface and solvent structure, thus minimizing the immunogenic potential of the mutations. This design strategy should be generally applicable to soluble globular proteins containing buried free-cysteine residues.

The antitumor agent 3-bromopyruvate has a short half-life at physiological conditions.

Science.gov (United States)

Glick, Matthew; Biddle, Perry; Jantzi, Josh; Weaver, Samantha; Schirch, Doug

2014-09-12

Clinical research is currently exploring the validity of the anti-tumor candidate 3-bromopyruvate (3-BP) as a novel treatment for several types of cancer. However, recent publications have overlooked rarely-cited earlier work about the instability of 3-BP and its decay to 3-hydroxypyruvate (3-HP) which have obvious implications for its mechanism of action against tumors, how it is administered, and for precautions when preparing solutions of 3-BP. This study found the first-order decay rate of 3-BP at physiological temperature and pH has a half-life of only 77 min. Lower buffer pH decreases the decay rate, while choice of buffer and concentration do not affect it. A method for preparing more stable solutions is also reported. Copyright © 2014 Elsevier Inc. All rights reserved.

Principles of proteome allocation are revealed using proteomic data and genome-scale models

DEFF Research Database (Denmark)

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.

2016-01-01

to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the "generalist" (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions......Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked...... of these sectors for the general stress response sigma factor sigma(S). Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally...

Differential proteomics of human seminal plasma: A potential target for searching male infertility marker proteins.

Science.gov (United States)

Tomar, Anil Kumar; Sooch, Balwinder Singh; Singh, Sarman; Yadav, Savita

2012-04-01

The clinical fertility tests, available in the market, fail to define the exact cause of male infertility in almost half of the cases and point toward a crucial need of developing better ways of infertility investigations. The protein biomarkers may help us toward better understanding of unknown cases of male infertility that, in turn, can guide us to find better therapeutic solutions. Many clinical attempts have been made to identify biomarkers of male infertility in sperm proteome but only few studies have targeted seminal plasma. Human seminal plasma is a rich source of proteins that are essentially required for development of sperm and successful fertilization. This viewpoint article highlights the importance of human seminal plasma proteome in reproductive physiology and suggests that differential proteomics integrated with functional analysis may help us in searching potential biomarkers of male infertility. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Half-Life Measurements in {sup 134}l

Energy Technology Data Exchange (ETDEWEB)

Berg, V; Hoeglund, Aa

1970-07-01

Properties of levels in I following the decay of {sup 13T}e have been investigated using a Ge(Li) detector and a double lens coincidence spectrometer. 4 new transitions were found. Half-lives of the lowest excited levels were measured with the following results: T{sub 1/2} (79.5 keV) = 1.62 {+-} 10 ns; T{sub 1/2} (181.1 keV) < 100 ps; T{sub 1/2} (210.8 keV) < 150 ps.

Dynamic adaptation of myocardial proteome during heart failure development

Science.gov (United States)

Poesch, Axel; Dörr, Marcus; Völker, Uwe; Grube, Karina; Hammer, Elke; Felix, Stephan B.

2017-01-01

Heart failure (HF) development is characterized by huge structural changes that are crucial for disease progression. Analysis of time dependent global proteomic adaptations during HF progression offers the potential to gain deeper insights in the disease development and identify new biomarker candidates. Therefore, hearts of TAC (transverse aortic constriction) and sham mice were examined by cardiac MRI on either day 4, 14, 21, 28, 42, and 56 after surgery (n = 6 per group/time point). At each time point, proteomes of the left (LV) and right ventricles (RV) of TAC and sham mice were analyzed by mass spectrometry (MS). In TAC mice, systolic LV heart function worsened from day 4 to day 14, remained on a stable level from day 14 to day 42, and showed a further pronounced decline at day 56. MS analysis identified in the LV 330 and in RV 246 proteins with altered abundance over time (TAC vs. sham, fc≥±2). Functional categorization of proteins disclosed the time-dependent alteration of different pathways. Heat shock protein beta-7 (HSPB7) displayed differences in abundance in tissue and serum at an early stage of HF. This study not only provides an overview of the time dependent molecular alterations during transition to HF, but also identified HSPB7 as a novel blood biomarker candidate for the onset of cardiac remodeling. PMID:28973020

Selective proteomic analysis of antibiotic-tolerant cellular subpopulations in pseudomonas aeruginosa biofilms

DEFF Research Database (Denmark)

Babin, Brett M.; Atangcho, Lydia; van Eldijk, Mark B.

2017-01-01

involved in central carbon metabolism. We differentiated the immediate proteomic response, characterized by an increase in flagellar motility, from the long-term adaptive strategy, which included the upregulation of purine synthesis. This targeted, selective analysis of a bacterial subpopulation...... amino acid tagging (BONCAT) method to enable selective proteomic analysis of a Pseudomonas aeruginosa biofilm subpopulation. Through controlled expression of a mutant methionyl-tRNA synthetase, we targeted BONCAT labeling to cells in the regions of biofilm microcolonies that showed increased tolerance...... demonstrates how the study of proteome dynamics can enhance our understanding of biofilm heterogeneity and antibiotic tolerance. IMPORTANCE Bacterial growth is frequently characterized by behavioral heterogeneity at the single-cell level. Heterogeneity is especially evident in the physiology of biofilms...

On the statistical evaluation of inconsistent measurement results illustrated on the example of the 90Sr half-life

International Nuclear Information System (INIS)

Zijp, W.L.

1985-12-01

The problem how to make an objective evaluation of inconsistent numerical observations made by different authors or laboratories on the same physical quantity is dealt with. The problem is treated in a practical way in the light of the example on the half-life of 90 Sr, and it is to some extent a response to a document by Gray (1985) on the same topic

Detection of ROS Induced Proteomic Signatures by Mass Spectrometry

Directory of Open Access Journals (Sweden)

Brian McDonagh

2017-07-01

Full Text Available Reversible and irreversible post-translational modifications (PTMs induced by endogenously generated reactive oxygen species (ROS in regulatory enzymes and proteins plays an essential role in cellular signaling. Almost all cellular processes including metabolism, transcription, translation and degradation have been identified as containing redox regulated proteins. Specific redox modifications of key amino acids generated by ROS offers a dynamic and versatile means to rapidly alter the activity or functional structure of proteins in response to biochemical, environmental, genetic and pathological perturbations. How the proteome responds to these stimuli is of critical importance in oxidant physiology, as it can regulate the cell stress response by reversible and irreversible PTMs, affecting protein activity and protein-protein interactions. Due to the highly labile nature of many ROS species, applying redox proteomics can provide a signature footprint of the ROS species generated. Ideally redox proteomic approaches would allow; (1 the identification of the specific PTM, (2 identification of the amino acid residue that is modified and (3 the percentage of the protein containing the PTM. New developments in MS offer the opportunity of a more sensitive targeted proteomic approach and retrospective data analysis. Subsequent bioinformatics analysis can provide an insight into the biochemical and physiological pathways or cell signaling cascades that are affected by ROS generation. This mini-review will detail current redox proteomic approaches to identify and quantify ROS induced PTMs and the subsequent effects on cellular signaling.

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry

Directory of Open Access Journals (Sweden)

Lindo Micheal

2003-08-01

Full Text Available Abstract Proteomics experiments typically involve protein or peptide separation steps coupled to the identification of many hundreds to thousands of peptides by mass spectrometry. Development of methodology and instrumentation in this field is proceeding rapidly, and effective software is needed to link the different stages of proteomic analysis. We have developed an application, proteogest, written in Perl that generates descriptive and statistical analyses of the biophysical properties of multiple (e.g. thousands protein sequences submitted by the user, for instance protein sequences inferred from the complete genome sequence of a model organism. The application also carries out in silico proteolytic digestion of the submitted proteomes, or subsets thereof, and the distribution of biophysical properties of the resulting peptides is presented. proteogest is customizable, the user being able to select many options, for instance the cleavage pattern of the digestion treatment or the presence of modifications to specific amino acid residues. We show how proteogest can be used to compare the proteomes and digested proteome products of model organisms, to examine the added complexity generated by modification of residues, and to facilitate the design of proteomics experiments for optimal representation of component proteins.

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data.

Science.gov (United States)

Hermjakob, Henning

2006-09-01

Proteomics is a key field of modern biomolecular research, with many small and large scale efforts producing a wealth of proteomics data. However, the vast majority of this data is never exploited to its full potential. Even in publicly funded projects, often the raw data generated in a specific context is analysed, conclusions are drawn and published, but little attention is paid to systematic documentation, archiving, and public access to the data supporting the scientific results. It is often difficult to validate the results stated in a particular publication, and even simple global questions like "In which cellular contexts has my protein of interest been observed?" can currently not be answered with realistic effort, due to a lack of standardised reporting and collection of proteomics data. The Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organisation (HUPO), defines community standards for data representation in proteomics to facilitate systematic data capture, comparison, exchange and verification. In this article we provide an overview of PSI organisational structure, activities, and current results, as well as ways to get involved in the broad-based, open PSI process.

Analysis of proteome dynamics inside the silk gland lumen of Bombyx mori

Science.gov (United States)

Dong, Zhaoming; Zhao, Ping; Zhang, Yan; Song, Qianru; Zhang, Xiaolu; Guo, Pengchao; Wang, Dandan; Xia, Qingyou

2016-01-01

The silk gland is the only organ where silk proteins are synthesized and secreted in the silkworm, Bombyx mori. Silk proteins are stored in the lumen of the silk gland for around eight days during the fifth instar. Determining their dynamic changes is helpful for clarifying the secretion mechanism of silk proteins. Here, we identified the proteome in the silk gland lumen using liquid chromatography–tandem mass spectrometry, and demonstrated its changes during two key stages. From day 5 of the fifth instar to day 1 of wandering, the abundances of fibroins, sericins, seroins, and proteins of unknown functions increased significantly in different compartments of the silk gland lumen. As a result, these accumulated proteins constituted the major cocoon components. In contrast, the abundances of enzymes and extracellular matrix proteins decreased in the silk gland lumen, suggesting that they were not the structural constituents of silk. Twenty-five enzymes may be involved in the regulation of hormone metabolism for proper silk gland function. In addition, the metabolism of other non-proteinous components such as chitin and pigment were also discussed in this study. PMID:27102218

Making proteomics data accessible and reusable: current state of proteomics databases and repositories.

Science.gov (United States)

Perez-Riverol, Yasset; Alpi, Emanuele; Wang, Rui; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-03-01

Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mapping Protein-Protein Interactions by Quantitative Proteomics

DEFF Research Database (Denmark)

Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

2010-01-01

spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

Takagi-Sugeno Fuzzy Model of a One-Half Semiactive Vehicle Suspension: Lateral Approach

Directory of Open Access Journals (Sweden)

L. C. Félix-Herrán

2015-01-01

Full Text Available This work presents a novel semiactive model of a one-half lateral vehicle suspension. The contribution of this research is the inclusion of actuator dynamics (two magnetorheological nonlinear dampers in the modelling, which means that more realistic outcomes will be obtained, because, in real life, actuators have physical limitations. Takagi-Sugeno (T-S fuzzy approach is applied to a four-degree-of-freedom (4-DOF lateral one-half vehicle suspension. The system has two magnetorheological (MR dampers, whose numerical values come from a real characterization. T-S allows handling suspension’s components and actuator’s nonlinearities (hysteresis, saturation, and viscoplasticity by means of a set of linear subsystems interconnected via fuzzy membership functions. Due to their linearity, each subsystem can be handled with the very well-known control theory, for example, stability and performance indexes (this is an advantage of the T-S approach. To the best of authors’ knowledge, reported work does not include the aforementioned nonlinearities in the modelling. The generated model is validated via a case of study with simulation results. This research is paramount because it introduces a more accurate (the actuator dynamics, a complex nonlinear subsystem model that could be applied to one-half vehicle suspension control purposes. Suspension systems are extremely important for passenger comfort and stability in ground vehicles.

Proteomics approaches shed new light on hibernation physiology.

Science.gov (United States)

Grabek, Katharine R; Martin, Sandra L; Hindle, Allyson G

2015-08-01

The broad phylogenetic distribution and rapid phenotypic transitions of mammalian hibernators imply that hibernation is accomplished by differential expression of common genes. Traditional candidate gene approaches have thus far explained little of the molecular mechanisms underlying hibernation, likely due to (1) incomplete and imprecise sampling of a complex phenotype, and (2) the forming of hypotheses about which genes might be important based on studies of model organisms incapable of such dynamic physiology. Unbiased screening approaches, such as proteomics, offer an alternative means to discover the cellular underpinnings that permit successful hibernation and may reveal previously overlooked, important pathways. Here, we review the findings that have emerged from proteomics studies of hibernation. One striking feature is the stability of the proteome, especially across the extreme physiological shifts of torpor-arousal cycles during hibernation. This has led to subsequent investigations of the role of post-translational protein modifications in altering protein activity without energetically wasteful removal and rebuilding of protein pools. Another unexpected finding is the paucity of universal proteomic adjustments across organ systems in response to the extreme metabolic fluctuations despite the universality of their physiological challenges; rather each organ appears to respond in a unique, tissue-specific manner. Additional research is needed to extend and synthesize these results before it will be possible to address the whole body physiology of hibernation.

Measurement of the half-life of 60Fe using the Argonne FN tandem-superconducting Linac system as an accelerator mass spectrometer

International Nuclear Information System (INIS)

Kutschera, W.; Billquist, P.J.; Frekers, D.

1983-01-01

An experiment to improve the accuracy in the half-life value of 60 Fe by measuring both the amount of 60 Fe nuclei and the decay-rate of a spallation produced sample using the relation dN/dt = -lambda N is briefly discussed

The effective and environmental half-life of 137Cs at Coral Islands at the former US nuclear test site

International Nuclear Information System (INIS)

Robison, William L.; Conrado, Cynthia L.; Bogen, Kenneth T.; Stoker, A. Carol

2003-01-01

The United States (US) conducted nuclear weapons testing from 1946 to 1958 at Bikini and Enewetak Atolls in the northern Marshall Islands. Based on previous detailed dose assessments for Bikini, Enewetak, Rongelap, and Utirik Atolls over a period of 28 years, cesium-137 ( 137 Cs) at Bikini Atoll contributes about 85-89% of the total estimated dose through the terrestrial food chain as a result of uptake of 137 Cs by food crops. The estimated integral 30, 50, and 70-year doses were based on the radiological decay of 137 Cs (30-year half-life) and other radionuclides. However, there is a continuing inventory of 137 Cs and 90 Sr in the fresh water portion of the groundwater at all contaminated atolls even though the turnover rate of the fresh groundwater is about 5 years. This is evidence that a portion of the soluble fraction of 137 Cs and 90 Sr inventory in the soil is lost by transport to groundwater when rainfall is heavy enough to cause recharge of the lens, resulting in loss of 137 Cs from the soil column and root zone of the plants. This loss is in addition to that caused by radioactive decay. The effective rate of loss was determined by two methods: (1) indirectly, from time-dependent studies of the 137 Cs concentration in leaves of Pisonia grandis, Guettarda specosia, Tournefortia argentea (also called Messerschmidia), Scaevola taccada, and fruit from Pandanus and coconut trees (Cocos nucifera L.), and (2) more directly, by evaluating the 137 Cs/ 90 Sr ratios at Bikini Atoll. The mean (and its lower and upper 95% confidence limits) for effective half-life and for environmental-loss half-life (ELH) based on all the trees studied on Rongelap, Bikini, and Enewetak Atolls are 8.5 years (8.0 years, 9.8 years), and 12 years (11 years, 15 years), respectively. The ELH based on the 137 Cs/ 90 Sr ratios in soil in 1987 relative to the 137 Cs/ 90 Sr ratios at the time of deposition in 1954 is less than 17 years. The magnitude of the decrease below 17 years depends on

The effective and environmental half-life of 137Cs at Coral Islands at the former US nuclear test site.

Science.gov (United States)

Robison, William L; Conrado, Cynthia L; Bogen, Kenneth T; Stoker, A Carol

2003-01-01

The United States (US) conducted nuclear weapons testing from 1946 to 1958 at Bikini and Enewetak Atolls in the northern Marshall Islands. Based on previous detailed dose assessments for Bikini, Enewetak, Rongelap, and Utirik Atolls over a period of 28 years, cesium-137 (137Cs) at Bikini Atoll contributes about 85-89% of the total estimated dose through the terrestrial food chain as a result of uptake of 137Cs by food crops. The estimated integral 30, 50, and 70-year doses were based on the radiological decay of 137Cs (30-year half-life) and other radionuclides. However, there is a continuing inventory of 137Cs and 90Sr in the fresh water portion of the groundwater at all contaminated atolls even though the turnover rate of the fresh groundwater is about 5 years. This is evidence that a portion of the soluble fraction of 137Cs and 90Sr inventory in the soil is lost by transport to groundwater when rainfall is heavy enough to cause recharge of the lens, resulting in loss of 137Cs from the soil column and root zone of the plants. This loss is in addition to that caused by radioactive decay. The effective rate of loss was determined by two methods: (1) indirectly, from time-dependent studies of the 137Cs concentration in leaves of Pisonia grandis, Guettarda specosia, Tournefortia argentea (also called Messerschmidia), Scaevola taccada, and fruit from Pandanus and coconut trees (Cocos nucifera L.), and (2) more directly, by evaluating the 137Cs/90Sr ratios at Bikini Atoll. The mean (and its lower and upper 95% confidence limits) for effective half-life and for environmental-loss half-life (ELH) based on all the trees studied on Rongelap, Bikini, and Enewetak Atolls are 8.5 years (8.0 years, 9.8 years), and 12 years (11 years, 15 years), respectively. The ELH based on the 137Cs/90Sr ratios in soil in 1987 relative to the 137Cs/90Sr ratios at the time of deposition in 1954 is less than 17 years. The magnitude of the decrease below 17 years depends on the ELH for 90Sr

Proteomics in medical microbiology.

Science.gov (United States)

Cash, P

2000-04-01

The techniques of proteomics (high resolution two-dimensional electrophoresis and protein characterisation) are widely used for microbiological research to analyse global protein synthesis as an indicator of gene expression. The rapid progress in microbial proteomics has been achieved through the wide availability of whole genome sequences for a number of bacterial groups. Beyond providing a basic understanding of microbial gene expression, proteomics has also played a role in medical areas of microbiology. Progress has been made in the use of the techniques for investigating the epidemiology and taxonomy of human microbial pathogens, the identification of novel pathogenic mechanisms and the analysis of drug resistance. In each of these areas, proteomics has provided new insights that complement genomic-based investigations. This review describes the current progress in these research fields and highlights some of the technical challenges existing for the application of proteomics in medical microbiology. The latter concern the analysis of genetically heterogeneous bacterial populations and the integration of the proteomic and genomic data for these bacteria. The characterisation of the proteomes of bacterial pathogens growing in their natural hosts remains a future challenge.

Formaldehyde cross-linking and structural proteomics: Bridging the gap.

Science.gov (United States)

Srinivasa, Savita; Ding, Xuan; Kast, Juergen

2015-11-01

Proteins are dynamic entities constantly moving and altering their structures based on their functions and interactions inside and outside the cell. Formaldehyde cross-linking combined with mass spectrometry can accurately capture interactions of these rapidly changing biomolecules while maintaining their physiological surroundings. Even with its numerous established uses in biology and compatibility with mass spectrometry, formaldehyde has not yet been applied in structural proteomics. However, formaldehyde cross-linking is moving toward analyzing tertiary structure, which conventional cross-linkers have already accomplished. The purpose of this review is to describe the potential of formaldehyde cross-linking in structural proteomics by highlighting its applications, characteristics and current status in the field. Copyright © 2015 Elsevier Inc. All rights reserved.

Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry.

Science.gov (United States)

Ahmed, Farid E

2009-03-01

Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.

[Trends in participation in nonformal education in the second half of life : Increasing educational participation in retirement].

Science.gov (United States)

Wiest, Maja; Hoffmann, Madlain; Widany, Sarah; Kaufmann, Katrin

2017-05-22

Research on nonformal education often focuses on participation within employment. Participation of workers decreases with age; however, recent studies show an increase in participation in nonformal education of older workers. It remains, however, unclear if this trend spills over to retirement. In the context of social change processes, trends in nonformal educational participation are analyzed. The study addresses employment and retirement as opportunity structures and investigates their impact on educational participation in the second half of life. Predictors of educational participation are modeled in logistic regression, including interaction effects. Analyses are based on cross-sectional data of the German Ageing Survey and covers 20,129 respondents aged 40-85 years (T 1 : 1996 n = 4838; T 2 : 2002 n = 3084; T 3 : 2008 n = 6205; T 4 : 2014 n = 6002). Educational level, age, gender, employment status, region, social integration, and subjective health predict participation in nonformal education for people aged 40 to 85 years. Employment as an opportunity structure has a constant impact on participation, whereas retirees' participation increases over the course of time. The increase of retirees' participation in nonformal education is discussed in the context of social change processes and connected to theoretical und empirical research gaps with regard to educational participation in the second half of life.

Dynamic changes in the date palm fruit proteome during development and ripening

KAUST Repository

Marondedze, Claudius; Gehring, Christoph A; Thomas, Ludivine

2014-01-01

in gel comparative proteomics combined with tandem mass spectrometry were used to study date fruit development and ripening. Total proteins were extracted using a phenol-based protocol. A total of 189 protein spots were differentially regulated (p≤0

The landscape of viral proteomics and its potential to impact human health

Energy Technology Data Exchange (ETDEWEB)

Oxford, Kristie L.; Wendler, Jason P.; McDermott, Jason E.; White III, Richard A.; Powell, Joshua D.; Jacobs, Jon M.; Adkins, Joshua N.; Waters, Katrina M.

2016-05-06

Translating the intimate discourse between viruses and their host cells during infection is a challenging but critical task for development of antiviral interventions and diagnostics. Viruses commandeer cellular processes at every step of their life cycle, altering expression of genes and proteins. Advances in mass spectrometry-based proteomic technologies are enhancing studies of viral pathogenesis by identifying virus-induced changes in the protein repertoire of infected cells or extracellular fluids. Interpretation of proteomics results using knowledge of cellular pathways and networks leads to identification of proteins that influence a range of infection processes, thereby focusing efforts for clinical diagnoses and therapeutics development. Herein we discuss applications of global proteomic studies of viral infections with the goal of providing a basis for improved studies that will benefit community-wide data integration and interpretation.

Analytical methods for proteome data obtained from SDS-PAGE multi-dimensional separation and mass spectrometry

Directory of Open Access Journals (Sweden)

Gun Wook Park

2010-03-01

Full Text Available For proteome analysis, various experimental protocols using mass spectrometry have been developed over thelast decade. The different protocols have differing performances and degrees of accuracy. Furthermore, the “best”protocol for a proteomic analysis of a sample depends on the purpose of the analysis, especially in connection withdisease proteomics, including biomarker discovery and therapeutics analyses of human serum or plasma. Theprotein complexity and the wide dynamic range of blood samples require high-dimensional separation technology.In this article, we review proteome analysis protocols in which both Sodium Dodecyl Sulfate-Polyacryl Amide GelElectrophoresis(SDS-PAGE and liquid chromatography are used for peptide and protein separations. Multidimensionalseparation technology supplies a high-quality dataset of tandem mass spectra and reveals signals fromlow-abundance proteins, although it can be time-consuming and laborious work. We survey shotgun proteomicsprotocols using SDS-PAGE and liquid chromatography and introduce bioinformatics tools for the analysis ofproteomics data. We also review efforts toward the biological interpretation of the proteome.

Is social stress in the first half of life detrimental to later physical and mental health in both men and women?

NARCIS (Netherlands)

Steverink, N.; Veenstra, R.; Oldehinkel, A.J.; Gans, R.O.B.; Rosmalen, J.G.M.

This study examined gender differences in the associations between affection-and status-related stressors encountered in the first half of life and physical and mental health problems later on. Based on the theory of Social Production Functions (SPF) two hypotheses have been formulated, which were

Proteomic profiling of the human T-cell nucleolus.

Science.gov (United States)

Jarboui, Mohamed Ali; Wynne, Kieran; Elia, Giuliano; Hall, William W; Gautier, Virginie W

2011-12-01

The nucleolus, site of ribosome biogenesis, is a dynamic subnuclear organelle involved in diverse cellular functions. The size, number and organisation of nucleoli are cell-specific and while it remains to be established, the nucleolar protein composition would be expected to reflect lineage-specific transcriptional regulation of rDNA genes and have cell-type functional components. Here, we describe the first characterisation of the human T-cell nucleolar proteome. Using the Jurkat T-cell line and a reproducible organellar proteomic approach, we identified 872 nucleolar proteins. In addition to ribosome biogenesis and RNA processing networks, network modeling and topological analysis of nucleolar proteome revealed distinct macromolecular complexes known to orchestrate chromatin structure and to contribute to the regulation of gene expression, replication, recombination and repair, and chromosome segregation. Furthermore, among our dataset, we identified proteins known to functionally participate in T-cell biology, including RUNX1, ILF3, ILF2, STAT3, LSH, TCF-1, SATB1, CTCF, HMGB3, BCLAF1, FX4L1, ZAP70, TIAM1, RAC2, THEMIS, LCP1, RPL22, TOPK, RETN, IFI-16, MCT-1, ISG15, and 14-3-3τ, which support cell-specific composition of the Jurkat nucleolus. Subsequently, the nucleolar localisation of RUNX1, ILF3, STAT3, ZAP70 and RAC2 was further validated by Western Blot analysis and immunofluorescence microscopy. Overall, our T-cell nucleolar proteome dataset not only further expands the existing repertoire of the human nucleolar proteome but support a cell type-specific composition of the nucleolus in T cell and highlights the potential roles of the nucleoli in lymphocyte biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

Determination of half-life of Ks0

International Nuclear Information System (INIS)

Urrutia, Z.; Felix, J.

1999-01-01

In a K s 0 high statistics sample, created in pp reactions at 27.5 GeV, we determined K s 0 mean life to be (0.893 ± 0.006) x 10 -10 s. This result agrees, inside experimental errors, with the world wide accepted value. In this paper we describe the experimental details and the used technique to measure K s 0 mean life. (Author)

Proteomic analysis of the Theileria annulata schizont.

OpenAIRE

Witschi Marc; Xia D; Sanderson Sandy; Baumgartner Martin; Wastling Jonathan; Dobbelaere Dirk

2013-01-01

The apicomplexan parasite, Theileria annulata, is the causative agent of tropical theileriosis, a devastating lymphoproliferative disease of cattle. The schizont stage transforms bovine leukocytes and provides an intriguing model to study host/pathogen interactions. The genome of T. annulata has been sequenced and transcriptomic data are rapidly accumulating. In contrast, little is known about the proteome of the schizont, the pathogenic, transforming life cycle stage of the parasite. Using o...

Increased volume of distribution for recombinant activated factor VII and longer plasma-derived factor VII half-life may explain their long lasting prophylactic effect.

Science.gov (United States)

Mathijssen, Natascha C J; Masereeuw, Rosalinde; Holme, Pal Andre; van Kraaij, Marian G J; Laros-van Gorkom, Britta A P; Peyvandi, Flora; van Heerde, Waander L

2013-08-01

Prophylaxis with plasma-derived or recombinant activated factor VII is beneficial in severe factor VII deficiency. To understand why prophylactic treatment with both products is efficacious, we conducted a pharmacokinetic study. Ten factor VII deficient patients were treated with either recombinant activated (20 μg/kg) or plasma-derived (25 IU/kg) factor VII in a cross-over design. Pharmacokinetic parameters were analyzed through activated factor VII activity, factor VII clotting activity, and factor VII antigen levels on depicted time points. Factor VII activity half-lifes, determined by non-compartmental and one-compartmental analysis (results in brackets), were shorter for recombinant activated (1.4h; 0.7h) than for plasma-derived factor VII (6.8h; 3.2h); both recombinant activated (5.1h; 2.1h and plasma-derived factor VII (5.8h; 3.2h) resulted in longer half-lives of factor VII antigen. Activated factor VII half-lives (based on activated factor VII activity levels) were significantly higher compared to factor VII clotting activity (1.6h; 0.9h). Volumes of distribution were significantly higher for activated factor VII (236 ml/kg; 175 ml/kg, measured by activated factor VII) as compared to plasma-derived factor VII (206 ml/kg; 64 ml/kg, measured by factor FVII activity), suggesting a plasma- and extracellular fluid distribution for recombinant activated factor VII. Recombinant activated factor VII showed significantly shorter half-lifes than plasma-derived factor VII. Volumes of distribution were significantly higher for treatment with recombinant activated factor VII. The longer half-life for plasma-derived factor VII, compared to recombinant activated factor VII, and the increased volume of distribution for recombinant activated factor VII, compared to plasma-derived factor VII may further elucidate the beneficial effect of prophylactic treatment of both products. Copyright © 2013 Elsevier Ltd. All rights reserved.

Data from proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis

Directory of Open Access Journals (Sweden)

Yongxin Yang

2015-06-01

Full Text Available Milk fat globules memebrane (MFGM-enriched proteomes from Holstein, Jersey, yak, buffalo, goat, camel, horse, and human were extracted and identified by an iTRAQ quantification proteomic approach. Proteomes data were analyzed by bioinformatic and multivariate statistical analysis and used to present the characteristic traits of the MFGM proteins among the studied mammals. The data of this study are also related to the research article “Proteomic characterization and comparison of mammalian milk fat globule proteomes by iTRAQ analysis” in the Journal of Proteomics [1].

Bacterial membrane proteomics.

Science.gov (United States)

Poetsch, Ansgar; Wolters, Dirk

2008-10-01

About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

New limit on the half-life of 78Kr with respect to the 2K(2ν)-capture decay mode

International Nuclear Information System (INIS)

Gavriljuk, Ju.M.; Kuzminov, V.V.; Osetrova, N.Ya.; Ratkevich, S.S.

2000-01-01

The features of data accumulated for 1817 h in an experimental search for the 2K(2ν)-capture mode of 78 Kr decay are discussed. A new limit on the half-life for this decay is found: T 1sol2 ≥ 2.3 x 10 20 yr (at a 90% C.L.)

From genomes to vaccines via the proteome

Directory of Open Access Journals (Sweden)

R Alan Wilson

2004-08-01

Full Text Available An effective vaccine against schistosomiasis mansoni would be a valuable control tool and the high levels of protection elicited in rodents and primates by radiation-attenuated cercariae provide proof of principle. A major obstacle to vaccine development is the difficulty of identifying the antigens that mediate protection, not least because of the size of the genome at 280Mb DNA encoding 14,000 to 20,000 genes. The technologies collectively called proteomics, including 2D electrophoresis, liquid chromatography and mass spectrometry, now permit any protein to be identified provided there is extensive DNA data, and preferably a genome sequence. Applied to soluble (cytosolic proteins from schistosomes, proteomics reveals the great similarity in composition between life cycle stages, with several WHO vaccine candidates amongst the most abundant constituents. The proteomic approach has been successfully applied to identify the secretions used by cercaria to penetrate host skin, the gut secretions of adult worms and the proteins exposed on the tegument surface. Soluble proteins can also be separated by 2D electrophoresis before western blotting to identify the full range of antigenic targets present in a parasite preparation. The next step is to discover which target proteins represent the weak points in the worm's defences.

Development and standardization of multiplexed antibody microarrays for use in quantitative proteomics

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Sorette M

2004-12-01

Full Text Available Abstract Background Quantitative proteomics is an emerging field that encompasses multiplexed measurement of many known proteins in groups of experimental samples in order to identify differences between groups. Antibody arrays are a novel technology that is increasingly being used for quantitative proteomics studies due to highly multiplexed content, scalability, matrix flexibility and economy of sample consumption. Key applications of antibody arrays in quantitative proteomics studies are identification of novel diagnostic assays, biomarker discovery in trials of new drugs, and validation of qualitative proteomics discoveries. These applications require performance benchmarking, standardization and specification. Results Six dual-antibody, sandwich immunoassay arrays that measure 170 serum or plasma proteins were developed and experimental procedures refined in more than thirty quantitative proteomics studies. This report provides detailed information and specification for manufacture, qualification, assay automation, performance, assay validation and data processing for antibody arrays in large scale quantitative proteomics studies. Conclusion The present report describes development of first generation standards for antibody arrays in quantitative proteomics. Specifically, it describes the requirements of a comprehensive validation program to identify and minimize antibody cross reaction under highly multiplexed conditions; provides the rationale for the application of standardized statistical approaches to manage the data output of highly replicated assays; defines design requirements for controls to normalize sample replicate measurements; emphasizes the importance of stringent quality control testing of reagents and antibody microarrays; recommends the use of real-time monitors to evaluate sensitivity, dynamic range and platform precision; and presents survey procedures to reveal the significance of biomarker findings.

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.

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Edward J O'Brien

2016-06-01

Full Text Available The costs and benefits of protein expression are balanced through evolution. Expression of un-utilized protein (that have no benefits in the current environment incurs a quantifiable fitness costs on cellular growth rates; however, the magnitude and variability of un-utilized protein expression in natural settings is unknown, largely due to the challenge in determining environment-specific proteome utilization. We address this challenge using absolute and global proteomics data combined with a recently developed genome-scale model of Escherichia coli that computes the environment-specific cost and utility of the proteome on a per gene basis. We show that nearly half of the proteome mass is unused in certain environments and accounting for the cost of this unused protein expression explains >95% of the variance in growth rates of Escherichia coli across 16 distinct environments. Furthermore, reduction in unused protein expression is shown to be a common mechanism to increase cellular growth rates in adaptive evolution experiments. Classification of the unused protein reveals that the unused protein encodes several nutrient- and stress- preparedness functions, which may convey fitness benefits in varying environments. Thus, unused protein expression is the source of large and pervasive fitness costs that may provide the benefit of hedging against environmental change.

Real-time RT-PCR analysis of mRNA decay: half-life of Beta-actin mRNA in human leukemia CCRF-CEM and Nalm-6 cell lines

Directory of Open Access Journals (Sweden)

Barredo Julio C

2002-03-01

Full Text Available Abstract Background We describe an alternative method to determine mRNA half-life (t1/2 based on the Real-Time RT-PCR procedure. This approach was evaluated by using the β-actin gene as a reference molecule for measuring of mRNA stability. Results Human leukemia Nalm-6 and CCRF-CEM cells were treated with various concentrations of Actinomycin D to block transcription and aliquots were removed periodically. Total RNA was isolated and quantified using the RiboGreen® fluorescent dye with the VersaFluor Fluorometer System. One μg of total RNA was reverse transcribed and used as template for the amplification of a region of the β-actin gene (231 bp. To generate the standard curve, serial ten-fold dilutions of the pBactin-231 vector containing the cDNA amplified fragment were employed, β-actin mRNAs were quantified by Real-Time RT-PCR using the SYBR® Green I fluorogenic dye and data analyzed using the iCycle iQ system software. Using this method, the β-actin mRNA exhibited a half-life of 6.6 h and 13.5 h in Nalm-6 and CCRF-CEM cells, respectively. The t1/2 value obtained for Nalm-6 is comparable to those estimated from Northern blot studies, using normal human leukocytes (5.5 h. Conclusions We have developed a rapid, sensitive, and reliable method based on Real-Time RT-PCR for measuring mRNA half-life. Our results confirm that β-actin mRNA half-life can be affected by the cellular growth rate.

Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples

NARCIS (Netherlands)

Horvatovich, Peter; Hoekman, Berend; Govorukhina, Natalia; Bischoff, Rainer

Multidimensional chromatography coupled to mass spectrometry (LC(n)-MS) provides more separation power and an extended measured dynamic concentration range to analyse complex proteomics samples than one dimensional liquid chromatography coupled to mass spectrometry (1D-LC-MS). This review gives an

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

DEFF Research Database (Denmark)

Geyer, Philipp E; Wewer Albrechtsen, Nicolai J; Tyanova, Stefka

2016-01-01

Sustained weight loss is a preferred intervention in a wide range of metabolic conditions, but the effects on an individual's health state remain ill-defined. Here, we investigate the plasma proteomes of a cohort of 43 obese individuals that had undergone 8 weeks of 12% body weight loss followed...... by a year of weight maintenance. Using mass spectrometry-based plasma proteome profiling, we measured 1,294 plasma proteomes. Longitudinal monitoring of the cohort revealed individual-specific protein levels with wide-ranging effects of losing weight on the plasma proteome reflected in 93 significantly...

Translational plant proteomics: a perspective.

Science.gov (United States)

Agrawal, Ganesh Kumar; Pedreschi, Romina; Barkla, Bronwyn J; Bindschedler, Laurence Veronique; Cramer, Rainer; Sarkar, Abhijit; Renaut, Jenny; Job, Dominique; Rakwal, Randeep

2012-08-03

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics. Copyright © 2012 Elsevier B.V. All rights reserved.

Dynamic imaging with coincidence gamma camera

International Nuclear Information System (INIS)

Elhmassi, Ahmed

2008-01-01

In this paper we develop a technique to calculate dynamic parameters from data acquired using gamma-camera PET (gc PET). Our method is based on an algorithm development for dynamic SPECT, which processes all decency projection data simultaneously instead of reconstructing a series of static images individually. The algorithm was modified to account for the extra data that is obtained with gc PET (compared with SPEC). The method was tested using simulated projection data for both a SPECT and a gc PET geometry. These studies showed the ability of the code to reconstruct simulated data with a varying range of half-lives. The accuracy of the algorithm was measured in terms of the reconstructed half-life and initial activity for the simulated object. The reconstruction of gc PET data showed improvement in half-life and activity compared to SPECT data of 23% and 20%, respectively (at 50 iterations). The gc PET algorithm was also tested using data from an experimental phantom and finally, applied to a clinical dataset, where the algorithm was further modified to deal with the situation where the activity in certain pixels decreases and then increases during the acquisition. (author)

Proteomics in Traditional Chinese Medicine with an Emphasis on Alzheimer’s Disease

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Yanuar Alan Sulistio

2015-01-01

Full Text Available In recent years, there has been an increasing worldwide interest in traditional Chinese medicine (TCM. This increasing demand for TCM needs to be accompanied by a deeper understanding of the mechanisms of action of TCM-based therapy. However, TCM is often described as a concept of Chinese philosophy, which is incomprehensible for Western medical society, thereby creating a gap between TCM and Western medicine (WM. In order to meet this challenge, TCM research has applied proteomics technologies for exploring the mechanisms of action of TCM treatment. Proteomics enables TCM researchers to oversee various pathways that are affected by treatment, as well as the dynamics of their interactions with one another. This review discusses the utility of comparative proteomics to better understand how TCM treatment may be used as a complementary therapy for Alzheimer’s disease (AD. Additionally, we review the data from comparative AD-related TCM proteomics studies and establish the relevance of the data with available AD hypotheses, most notably regarding the ubiquitin proteasome system (UPS.

Proteomics as a tool to explore human milk in health and disease.

Science.gov (United States)

Roncada, Paola; Stipetic, Laurence H; Bonizzi, Luigi; Burchmore, Richard J S; Kennedy, Malcolm W

2013-08-02

Proteins in milk have wide range of functions, they are carriers of minerals or chemically vulnerable and insoluble vitamins and other compounds, stabilisers of large aggregates or micelles of lipids, and components of both innate and acquired immune defence systems. Together with other components of milk, proteins may also contribute to the selection and establishment of appropriate microbiome in the gut of the infant. The proteome of mammalian milk is now known to be dynamic and changes radically with time after birth from colostrum to mature lactation. Significantly, immune and innate defence proteins appear in milk during infection of the mammary gland and possibly also during systemic infections. The understanding of the human milk proteome and how it changes with time during lactation and in disease is developing rapidly, and is to a large extent informed by proteomics of the milks of non-human mammals, domestic animals in particular. We review general methods now being applied for proteomic analysis of human milk. Moreover we place emphasis on how the milk proteome may change in different ways in response to disease, mastitis in particular, how such changes may be specific to pathogen types, and we give some insights about evolution. Copyright © 2013 Elsevier B.V. All rights reserved.

Decomposing changes in life expectancy: Compression versus shifting mortality

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Marie-Pier Bergeron-Boucher

2015-09-01

Full Text Available Background: In most developed countries, mortality reductions in the first half of the 20th century were highly associated with changes in lifespan disparities. In the second half of the 20th century, changes in mortality are best described by a shift in the mortality schedule, with lifespan variability remaining nearly constant. These successive mortality dynamics are known as compression and shifting mortality, respectively. Objective: To understand the effect of compression and shifting dynamics on mortality changes, we quantify the gains in life expectancy due to changes in lifespan variability and changes in the mortality schedule, respectively. Methods: We introduce a decomposition method using newly developed parametric expressions of the force of mortality that include the modal age at death as one of their parameters. Our approach allows us to differentiate between the two underlying processes in mortality and their dynamics. Results: An application of our methodology to the mortality of Swedish females shows that, since the mid-1960s, shifts in the mortality schedule were responsible for more than 70Š of the increase in life expectancy. Conclusions: The decomposition method allows differentiation between both underlying mortality processes and their respective impact on life expectancy, and also determines when and how one process has replaced the other.

Proteome dynamics and physiological responses to short-term salt stress in Leymus chinensis leaves.

Directory of Open Access Journals (Sweden)

Jikai Li

Full Text Available Salt stress is becoming an increasing threat to global agriculture. In this study, physiological and proteomics analysis were performed using a salt-tolerant grass species, Leymus chinensis (L. chinensis. The aim of this study is to understand the potential mechanism of salt tolerance in L. chinensis that used for crop molecular breeding. A series of short-term (<48 h NaCl treatments (0 ~ 700 mM were conducted. Physiological data indicated that the root and leaves growth were inhibited, chlorophyll contents decreased, while hydraulic conductivity, proline, sugar and sucrose were accumulated under salt stress. For proteomic analysis, we obtained 274 differentially expressed proteins in response to NaCl treatments. GO analysis revealed that 44 out of 274 proteins are involved in the biosynthesis of amino acids and carbon metabolism. Our findings suggested that L. chinensis copes with salt stress by stimulating the activities of POD, SOD and CAT enzymes, speeding up the reactions of later steps of citrate cycle, and synthesis of proline and sugar. In agreement with our physiological data, proteomic analysis also showed that salt stress depress the expression of photosystem relevant proteins, Calvin cycle, and chloroplast biosynthesis.

Contribution of MS-based proteomics to the understanding of Herpes Simplex Virus type 1 interaction with host cells

Directory of Open Access Journals (Sweden)

Enrique eSantamaría

2012-03-01

Full Text Available Like other DNA viruses, Herpes Simplex Virus type 1 (HSV-1 replicates and proliferates in host cells continuously modulating the host molecular environment. Following a sophisticated temporal expression pattern, HSV-1 encodes at least 89 multifunctional proteins that interplay with and modify the host cell proteome. During the last decade, advances in mass spectrometry applications coupled to the development of proteomic separation methods have allowed to partially monitor the impact of HSV-1 infection in human cells. In this review, we discuss the current use of different proteome fractionation strategies to define HSV-1 targets on two major application areas: i viral protein interactomics to decipher viral protein interactions in host cells and ii differential quantitative proteomics to analyse the virally induced changes in the cellular proteome. Moreover, we will also discuss the potential application of high throughput proteomic approaches to study global proteome dynamics and also post-translational modifications in HSV-1-infected cells, what will greatly improved our molecular knowledge of HSV-1 infection.

Half-life distribution table of radioactive nuclei; Table de distribution des periodes des noyaux radioactifs

Energy Technology Data Exchange (ETDEWEB)

Gugenberger, P [Commissariat a l' Energie Atomique, Saclay(France). Centre d' Etudes Nucleaires

1954-07-01

This table allows to identify an element if its period is known. Data for this table were taken from the half-life values adopted by Hollander, PERLMAN and SEABORG (Rev. mod. Phys., 1953, 22 number 2). Moreover for each nucleus, the mass number, the charge number and the type of decay are given in the table. (author) [French] Cette table permet l'identification d'un element dont la periode est connue. Elle a ete etablie en utilisant les valeurs des periodes donnees par HOLLANDER, PERLMAN et SEABORG dans Rev. mod. Phys., 1953, 25 numero 2. On y trouve en outre, pour chaque nuclide, les caracteristiques suivantes: Z, A, modes de desintegration. (auteur)

Half-life distribution table of radioactive nuclei; Table de distribution des periodes des noyaux radioactifs

Energy Technology Data Exchange (ETDEWEB)

Gugenberger, P. [Commissariat a l' Energie Atomique, Saclay(France). Centre d' Etudes Nucleaires

1954-07-01

This table allows to identify an element if its period is known. Data for this table were taken from the half-life values adopted by Hollander, PERLMAN and SEABORG (Rev. mod. Phys., 1953, 22 number 2). Moreover for each nucleus, the mass number, the charge number and the type of decay are given in the table. (author) [French] Cette table permet l'identification d'un element dont la periode est connue. Elle a ete etablie en utilisant les valeurs des periodes donnees par HOLLANDER, PERLMAN et SEABORG dans Rev. mod. Phys., 1953, 25 numero 2. On y trouve en outre, pour chaque nuclide, les caracteristiques suivantes: Z, A, modes de desintegration. (auteur)

Aptamer-based multiplexed proteomic technology for biomarker discovery.

Directory of Open Access Journals (Sweden)

Larry Gold

2010-12-01

Full Text Available The interrogation of proteomes ("proteomics" in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine.We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma. Our current assay measures 813 proteins with low limits of detection (1 pM median, 7 logs of overall dynamic range (~100 fM-1 µM, and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray. Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD. We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to rapidly discover unique protein signatures characteristic of various disease states.We describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.

Aptamer-based multiplexed proteomic technology for biomarker discovery.

Science.gov (United States)

Gold, Larry; Ayers, Deborah; Bertino, Jennifer; Bock, Christopher; Bock, Ashley; Brody, Edward N; Carter, Jeff; Dalby, Andrew B; Eaton, Bruce E; Fitzwater, Tim; Flather, Dylan; Forbes, Ashley; Foreman, Trudi; Fowler, Cate; Gawande, Bharat; Goss, Meredith; Gunn, Magda; Gupta, Shashi; Halladay, Dennis; Heil, Jim; Heilig, Joe; Hicke, Brian; Husar, Gregory; Janjic, Nebojsa; Jarvis, Thale; Jennings, Susan; Katilius, Evaldas; Keeney, Tracy R; Kim, Nancy; Koch, Tad H; Kraemer, Stephan; Kroiss, Luke; Le, Ngan; Levine, Daniel; Lindsey, Wes; Lollo, Bridget; Mayfield, Wes; Mehan, Mike; Mehler, Robert; Nelson, Sally K; Nelson, Michele; Nieuwlandt, Dan; Nikrad, Malti; Ochsner, Urs; Ostroff, Rachel M; Otis, Matt; Parker, Thomas; Pietrasiewicz, Steve; Resnicow, Daniel I; Rohloff, John; Sanders, Glenn; Sattin, Sarah; Schneider, Daniel; Singer, Britta; Stanton, Martin; Sterkel, Alana; Stewart, Alex; Stratford, Suzanne; Vaught, Jonathan D; Vrkljan, Mike; Walker, Jeffrey J; Watrobka, Mike; Waugh, Sheela; Weiss, Allison; Wilcox, Sheri K; Wolfson, Alexey; Wolk, Steven K; Zhang, Chi; Zichi, Dom

2010-12-07

The interrogation of proteomes ("proteomics") in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology and medicine. We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 µL of serum or plasma). Our current assay measures 813 proteins with low limits of detection (1 pM median), 7 logs of overall dynamic range (~100 fM-1 µM), and 5% median coefficient of variation. This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected. Proteins in complex matrices such as plasma are measured with a process that transforms a signature of protein concentrations into a corresponding signature of DNA aptamer concentrations, which is quantified on a DNA microarray. Our assay takes advantage of the dual nature of aptamers as both folded protein-binding entities with defined shapes and unique nucleotide sequences recognizable by specific hybridization probes. To demonstrate the utility of our proteomics biomarker discovery technology, we applied it to a clinical study of chronic kidney disease (CKD). We identified two well known CKD biomarkers as well as an additional 58 potential CKD biomarkers. These results demonstrate the potential utility of our technology to rapidly discover unique protein signatures characteristic of various disease states. We describe a versatile and powerful tool that allows large-scale comparison of proteome profiles among discrete populations. This unbiased and highly multiplexed search engine will enable the discovery of novel biomarkers in a manner that is unencumbered by our incomplete knowledge of biology, thereby helping to advance the next generation of evidence-based medicine.

Bioinformatical Analysis of Organ-Related (Heart, Brain, Liver, and Kidney and Serum Proteomic Data to Identify Protein Regulation Patterns and Potential Sepsis Biomarkers

Directory of Open Access Journals (Sweden)

Andreas Hohn

2018-01-01

Full Text Available During the last years, proteomic studies have revealed several interesting findings in experimental sepsis models and septic patients. However, most studies investigated protein alterations only in single organs or in whole blood. To identify possible sepsis biomarkers and to evaluate the relationship between protein alteration in sepsis affected organs and blood, proteomics data from the heart, brain, liver, kidney, and serum were analysed. Using functional network analyses in combination with hierarchical cluster analysis, we found that protein regulation patterns in organ tissues as well as in serum are highly dynamic. In the tissue proteome, the main functions and pathways affected were the oxidoreductive activity, cell energy generation, or metabolism, whereas in the serum proteome, functions were associated with lipoproteins metabolism and, to a minor extent, with coagulation, inflammatory response, and organ regeneration. Proteins from network analyses of organ tissue did not correlate with statistically significantly regulated serum proteins or with predicted proteins of serum functions. In this study, the combination of proteomic network analyses with cluster analyses is introduced as an approach to deal with high-throughput proteomics data to evaluate the dynamics of protein regulation during sepsis.

A novel exendin-4 human serum albumin fusion protein, E2HSA, with an extended half-life and good glucoregulatory effect in healthy rhesus monkeys

Energy Technology Data Exchange (ETDEWEB)

Zhang, Ling; Wang, Lin; Meng, Zhiyun; Gan, Hui; Gu, Ruolan; Wu, Zhuona; Gao, Lei; Zhu, Xiaoxia; Sun, Wenzhong; Li, Jian; Zheng, Ying; Dou, Guifang, E-mail: douguifang@vip.163.com

2014-03-07

Highlights: • E2HSA has an extended half-life and good plasma stability. • E2HSA could improve glucose-dependent insulin secretion. • E2HSA has excellent glucoregulatory effects in vivo. • E2HSA could potentially be used as a new long-acting GLP-1 receptor agonist for type 2 diabetes management. - Abstract: Glucagon-like peptide-1 (GLP-1) has attracted considerable research interest in terms of the treatment of type 2 diabetes due to their multiple glucoregulatory functions. However, the short half-life, rapid inactivation by dipeptidyl peptidase-IV (DPP-IV) and excretion, limits the therapeutic potential of the native incretin hormone. Therefore, efforts are being made to develop the long-acting incretin mimetics via modifying its structure. Here we report a novel recombinant exendin-4 human serum albumin fusion protein E2HSA with HSA molecule extends their circulatory half-life in vivo while still retaining exendin-4 biological activity and therapeutic properties. In vitro comparisons of E2HSA and exendin-4 showed similar insulinotropic activity on rat pancreatic islets and GLP-1R-dependent biological activity on RIN-m5F cells, although E2HSA was less potent than exendin-4. E2HSA had a terminal elimation half-life of approximate 54 h in healthy rhesus monkeys. Furthermore, E2HSA could reduce postprandial glucose excursion and control fasting glucose level, dose-dependent suppress food intake. Improvement in glucose-dependent insulin secretion and control serum glucose excursions were observed during hyperglycemic clamp test (18 h) and oral glucose tolerance test (42 h) respectively. Thus the improved physiological characterization of E2HSA make it a new potent anti-diabetic drug for type 2 diabetes therapy.

Multilayered proteomics reveals molecular switches dictating ligand-dependent EGFR trafficking

DEFF Research Database (Denmark)

Francavilla, Chiara; Papetti, Moreno; Rigbolt, Kristoffer T G

2016-01-01

, we devised an integrated multilayered proteomics approach (IMPA). We analyzed dynamic changes in the receptor interactome, ubiquitinome, phosphoproteome, and late proteome in response to both ligands in human cells by quantitative MS and identified 67 proteins regulated at multiple levels. We...... identified RAB7 phosphorylation and RCP recruitment to EGFR as switches for EGF and TGF-α outputs, controlling receptor trafficking, signaling duration, proliferation, and migration. By manipulating RCP levels or phosphorylation of RAB7 in EGFR-positive cancer cells, we were able to switch a TGF......-α-mediated response to an EGF-like response or vice versa as EGFR trafficking was rerouted. We propose IMPA as an approach to uncover fine-tuned regulatory mechanisms in cell signaling....

Proteomic and Microscopic Strategies towards the Analysis of the Cytoskeletal Networks in Major Neuropsychiatric Disorders

Directory of Open Access Journals (Sweden)

Joëlle V. F. Coumans

2016-04-01

Full Text Available Mental health disorders have become worldwide health priorities. It is estimated that in the next 20 years they will account for a 16 trillion United State dollars (US$ loss. Up to now, the underlying pathophysiology of psychiatric disorders remains elusive. Altered cytoskeleton proteins expression that may influence the assembly, organization and maintenance of cytoskeletal integrity has been reported in major depressive disorders, schizophrenia and to some extent bipolar disorders. The use of quantitative proteomics, dynamic microscopy and super-resolution microscopy to investigate disease-specific protein signatures holds great promise to improve our understanding of these disorders. In this review, we present the currently available quantitative proteomic approaches use in neurology, gel-based, stable isotope-labelling and label-free methodologies and evaluate their strengths and limitations. We also reported on enrichment/subfractionation methods that target the cytoskeleton associated proteins and discuss the need of alternative methods for further characterization of the neurocytoskeletal proteome. Finally, we present live cell imaging approaches and emerging dynamic microscopy technology that will provide the tools necessary to investigate protein interactions and their dynamics in the whole cells. While these areas of research are still in their infancy, they offer huge potential towards the understanding of the neuronal network stability and its modification across neuropsychiatric disorders.

Recent 5-year Findings and Technological Advances in the Proteomic Study of HIV-associated Disorders

OpenAIRE

Zhang, Lijun; Jia, Xiaofang; Jin, Jun-O; Lu, Hongzhou; Tan, Zhimi

2017-01-01

Human immunodeficiency virus-1 (HIV-1) mainly relies on host factors to complete its life cycle. Hence, it is very important to identify HIV-regulated host proteins. Proteomics is an excellent technique for this purpose because of its high throughput and sensitivity. In this review, we summarized current technological advances in proteomics, including general isobaric tags for relative and absolute quantitation (iTRAQ) and stable isotope labeling by amino acids in cell culture (SILAC), as wel...

Dual Constant Domain-Fab: A novel strategy to improve half-life and potency of a Met therapeutic antibody.

Science.gov (United States)

Cignetto, Simona; Modica, Chiara; Chiriaco, Cristina; Fontani, Lara; Milla, Paola; Michieli, Paolo; Comoglio, Paolo M; Vigna, Elisa

2016-06-01

The kinase receptor encoded by the Met oncogene is a sensible target for cancer therapy. The chimeric monovalent Fab fragment of the DN30 monoclonal antibody (MvDN30) has an odd mechanism of action, based on cell surface removal of Met via activation of specific plasma membrane proteases. However, the short half-life of the Fab, due to its low molecular weight, is a severe limitation for the deployment in therapy. This issue was addressed by increasing the Fab molecular weight above the glomerular filtration threshold through the duplication of the constant domains, in tandem (DCD-1) or reciprocally swapped (DCD-2). The two newly engineered molecules showed biochemical properties comparable to the original MvDN30 in vitro, acting as full Met antagonists, impairing Met phosphorylation and activation of downstream signaling pathways. As a consequence, Met-mediated biological responses were inhibited, including anchorage-dependent and -independent cell growth. In vivo DCD-1 and DCD-2 showed a pharmacokinetic profile significantly improved over the original MvDN30, doubling the circulating half-life and reducing the clearance. In pre-clinical models of cancer, generated by injection of tumor cells or implant of patient-derived samples, systemic administration of the engineered molecules inhibited the growth of Met-addicted tumors. Copyright © 2016 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

An improved method for determination of technetium-99m half-life for the quality assurance procedures of radiopharmaceuticals

International Nuclear Information System (INIS)

Abd Jalil Abd Hamid; Juhari Mohd Yusof; Zakaria Ibrahim; Wan Mohd Ferdaus Wan Ishak; Mohamad Hafiz Ahmad

2009-01-01

An improve method for identity tests of technetium-99m for the quality assurance procedures are presented. Computerized methods based on the least-squares of decay curve fitting for half-life estimation of technetium-99m was tested. Thus, least-squares method was employ as a decay curve fitting procedures in our software. Theoretical calculated half-life of technetium-99m for evaluation was performed for comparison. In Fig. 3 is shown, the decay curve fitting of a sample over one second counting time interval. The R2 value of the curve suggests that the time of the study was too short to obtain acceptable value. A similar measurement for another data set was done for a longer period of time and in Table 1 is shown a representative decay curve fitting. The value was found to be 6.006 hours with a discrepancy of -0.28% from the value taken from the literature. The value is in agreement with the literature for time interval greater than 2 seconds. The results obtained by this method show that the used of least-squares method for decay curve fitting are appropriate for routine identity tests. This confirmed that the least-squares method applied in our decay curve fitting software are remarkably improved and convenient for routine identity tests purposes. (Author)

Life history and population dynamics of an estuarine amphipod, Eriopisa chilkensis Chilton (Gammaridae)

Digital Repository Service at National Institute of Oceanography (India)

Aravind, N.P.; Sheeba, P.; Nair, K.K.C.; Achuthankutty, C.T.

Life history and Population Dynamics of an Estuarine Amphipod –Eriopisa chilkensis Chilton (Gammaridae) Nisha. P. Aravind, P. Sheeba, K.K.C. Nair and C.T.Achuthankutty* National Institute of Oceanography, Regional Centre, Cochin 682018, India... of laboratory data to the field suggests that E. chilkensis in Cochin estuary has a multivoltine life cycle. Key words: - Eriopisa chilkensis, Amphipoda, life cycle, population dynamics, Cochin estuary, India 2 1. Introduction Life-history traits of 214 amphipod...

Translational plant proteomics: A perspective

NARCIS (Netherlands)

Agrawal, G.K.; Pedreschi, R.; Barkla, B.J.; Bindschedler, L.V.; Cramer, R.; Sarkar, A.; Renaut, J.; Job, D.; Rakwal, R.

2012-01-01

Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic

Evolution of Clinical Proteomics and its Role in Medicine | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

NCI's Office of Cancer Clinical Proteomics Research authored a review of the current state of clinical proteomics in the peer-reviewed Journal of Proteome Research. The review highlights outcomes from the CPTC program and also provides a thorough overview of the different technologies that have pushed the field forward. Additionally, the review provides a vision for moving the field forward through linking advances in genomic and proteomic analysis to develop new, molecularly targeted interventions.

Dynamic changes in the date palm fruit proteome during development and ripening

KAUST Repository

Marondedze, Claudius

2014-08-06

Date palm (Phoenix dactylifera) is an economically important fruit tree in the Middle East and North Africa and is characterized by large cultivar diversity, making it a good model for studies on fruit development and other important traits. Here in gel comparative proteomics combined with tandem mass spectrometry were used to study date fruit development and ripening. Total proteins were extracted using a phenol-based protocol. A total of 189 protein spots were differentially regulated (p≤0.05). The identified proteins were classified into 14 functional categories. The categories with the most proteins were ‘disease and defense’ (16.5%) and ‘metabolism’ (15.4%). Twenty-nine proteins have not previously been identified in other fleshy fruits and 64 showed contrasting expression patterns in other fruits. Abundance of most proteins with a role in abiotic stress responses increased during ripening with the exception of heat shock proteins. Proteins with a role in anthocyanin biosynthesis, glycolysis, tricarboxylic acid cycle and cell wall degradation were upregulated particularly from the onset of ripening and during ripening. In contrast, expression of pentose phosphate- and photosynthesis-related proteins decreased during fruit maturation. Although date palm is considered a climacteric species, the analysis revealed downregulation of two enzymes involved in ethylene biosynthesis, suggesting an ethylene-independent ripening of ‘Barhi’ fruits. In summary, this proteomics study provides insights into physiological processes during date fruit development and ripening at the systems level and offers a reference proteome for the study of regulatory mechanisms that can inform molecular and biotechnological approaches to further improvements of horticultural traits including fruit quality and yield.

Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth

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Kai P. Law

2015-05-01

Full Text Available Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered.

Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth

Science.gov (United States)

Law, Kai P.; Han, Ting-Li; Tong, Chao; Baker, Philip N.

2015-01-01

Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered. PMID:26006232

Proteomics of Maize Root Development.

Science.gov (United States)

Hochholdinger, Frank; Marcon, Caroline; Baldauf, Jutta A; Yu, Peng; Frey, Felix P

2018-01-01

Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Proteomics of Maize Root Development

Directory of Open Access Journals (Sweden)

Frank Hochholdinger

2018-03-01

Full Text Available Maize forms a complex root system with structurally and functionally diverse root types that are formed at different developmental stages to extract water and mineral nutrients from soil. In recent years proteomics has been intensively applied to identify proteins involved in shaping the three-dimensional architecture and regulating the function of the maize root system. With the help of developmental mutants, proteomic changes during the initiation and emergence of shoot-borne, lateral and seminal roots have been examined. Furthermore, root hairs were surveyed to understand the proteomic changes during the elongation of these single cell type structures. In addition, primary roots have been used to study developmental changes of the proteome but also to investigate the proteomes of distinct tissues such as the meristematic zone, the elongation zone as well as stele and cortex of the differentiation zone. Moreover, subcellular fractions of the primary root including cell walls, plasma membranes and secreted mucilage have been analyzed. Finally, the superior vigor of hybrid seedling roots compared to their parental inbred lines was studied on the proteome level. In summary, these studies provide novel insights into the complex proteomic interactions of the elaborate maize root system during development.

Bioinformatics: future of life sciences

International Nuclear Information System (INIS)

Arif, R.; Ghafoor, M.; Saleem, M.; Baig, S.J.; Hassan, S.W.

2004-01-01

The vital part of our life or the basic unit of life is the cell. The cellular biomolecules function in a conjugate manner and this system provide us with the necessary elements of life, and the sciences that deals with nature function of the cell and it's molecular components are defined as life sciences. Vital subjects involved in maintaining the identity and functioning of cells are genomics and proteomics. (author)

Integrating cell biology and proteomic approaches in plants.

Science.gov (United States)

Takáč, Tomáš; Šamajová, Olga; Šamaj, Jozef

2017-10-03

Significant improvements of protein extraction, separation, mass spectrometry and bioinformatics nurtured advancements of proteomics during the past years. The usefulness of proteomics in the investigation of biological problems can be enhanced by integration with other experimental methods from cell biology, genetics, biochemistry, pharmacology, molecular biology and other omics approaches including transcriptomics and metabolomics. This review aims to summarize current trends integrating cell biology and proteomics in plant science. Cell biology approaches are most frequently used in proteomic studies investigating subcellular and developmental proteomes, however, they were also employed in proteomic studies exploring abiotic and biotic stress responses, vesicular transport, cytoskeleton and protein posttranslational modifications. They are used either for detailed cellular or ultrastructural characterization of the object subjected to proteomic study, validation of proteomic results or to expand proteomic data. In this respect, a broad spectrum of methods is employed to support proteomic studies including ultrastructural electron microscopy studies, histochemical staining, immunochemical localization, in vivo imaging of fluorescently tagged proteins and visualization of protein-protein interactions. Thus, cell biological observations on fixed or living cell compartments, cells, tissues and organs are feasible, and in some cases fundamental for the validation and complementation of proteomic data. Validation of proteomic data by independent experimental methods requires development of new complementary approaches. Benefits of cell biology methods and techniques are not sufficiently highlighted in current proteomic studies. This encouraged us to review most popular cell biology methods used in proteomic studies and to evaluate their relevance and potential for proteomic data validation and enrichment of purely proteomic analyses. We also provide examples of

Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.).

Science.gov (United States)

Hu, Guanjing; Koh, Jin; Yoo, Mi-Jeong; Pathak, Dharminder; Chen, Sixue; Wendel, Jonathan F

2014-12-01

Comparative proteomic analyses were performed to detail the evolutionary consequences of strong directional selection for enhanced fiber traits in modern upland cotton (Gossypium hirsutum L.). Using two complementary proteomic approaches, 2-DE and iTRAQ LC-MS/MS, fiber proteomes were examined for four representative stages of fiber development. Approximately 1,000 protein features were characterized using each strategy, collectively resulting in the identification and functional categorization of 1,223 proteins. Unequal contributions of homoeologous proteins were detected for over a third of the fiber proteome, but overall expression was balanced with respect to the genome-of-origin in the allopolyploid G. hirsutum. About 30% of the proteins were differentially expressed during fiber development within wild and domesticated cotton. Notably, domestication was accompanied by a doubling of protein developmental dynamics for the period between 10 and 20 days following pollination. Expression levels of 240 iTRAQ proteins and 293 2-DE spots were altered by domestication, collectively representing multiple cellular and metabolic processes, including metabolism, energy, protein synthesis and destination, defense and stress response. Analyses of homoeolog-specific expression indicate that duplicated gene products in cotton fibers can be differently regulated in response to selection. These results demonstrate the power of proteomics for the analysis of crop domestication and phenotypic evolution.

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-03-01

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

Precision measurement of the half-life of $^{109}$In in large and small lattice environments

CERN Multimedia

We propose to undertake high precision measurements of the half-life of $^{109}$In in large and small lattice environments to study the effect of compression on the electron capture nuclear decay rate. Such studies are of general interest having implications in many areas ranging from astrophysics to geophysics. At present, very little data is available on the change of electron capture decay rate under compression and the available data seems to indicate that the observed increase of the electron capture decay rate under compression is much greater than the predictions of the best available density functional calculations as obtained from TB-LMTO or WIEN2K codes. The proposed experiment should generate more data thus clarifying the experimental situation.

Differential alkylation-based redox proteomics--Lessons learnt.

Science.gov (United States)

Wojdyla, Katarzyna; Rogowska-Wrzesinska, Adelina

2015-12-01

Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S-sulfenylation are crucial mediators of intracellular redox signalling, with known associations to health and disease. Study of their functionalities has intensified thanks to the development of various analytical strategies, with particular contribution from differential alkylation-based proteomics methods. Presented here is a critical evaluation of differential alkylation-based strategies for the analysis of S-nitrosylation and S-sulfenylation. The aim is to assess the current status and to provide insights for future directions in the dynamically evolving field of redox proteomics. To achieve that we collected 35 original research articles published since 2010 and analysed them considering the following parameters, (i) resolution of modification site, (ii) quantitative information, including correction of modification levels by protein abundance changes and determination of modification site occupancy, (iii) throughput, including the amount of starting material required for analysis. The results of this meta-analysis are the core of this review, complemented by issues related to biological models and sample preparation in redox proteomics, including conditions for free thiol blocking and labelling of target cysteine oxoforms. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Science.gov (United States)

Yang, Laurence; Tan, Justin; O'Brien, Edward J; Monk, Jonathan M; Kim, Donghyuk; Li, Howard J; Charusanti, Pep; Ebrahim, Ali; Lloyd, Colton J; Yurkovich, James T; Du, Bin; Dräger, Andreas; Thomas, Alex; Sun, Yuekai; Saunders, Michael A; Palsson, Bernhard O

2015-08-25

Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma genitalium). Based on transcriptomics data across environmental and genetic backgrounds, the systems biology core proteome is significantly enriched in nondifferentially expressed genes and depleted in differentially expressed genes. Compared with the noncore, core gene expression levels are also similar across genetic backgrounds (two times higher Spearman rank correlation) and exhibit significantly more complex transcriptional and posttranscriptional regulatory features (40% more transcription start sites per gene, 22% longer 5'UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, validated by using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models; it de facto defines a paleome.

Proteomic profiling of an undefined microbial consortium cultured in fermented dairy manure: Methods development.

Science.gov (United States)

Hanson, Andrea J; Paszczynski, Andrzej J; Coats, Erik R

2016-03-01

The production of polyhydroxyalkanoates (PHA; bioplastics) from waste or surplus feedstocks using mixed microbial consortia (MMC) and aerobic dynamic feeding (ADF) is a growing field within mixed culture biotechnology. This study aimed to optimize a 2DE workflow to investigate the proteome dynamics of an MMC synthesizing PHA from fermented dairy manure. To mitigate the challenges posed to effective 2DE by this complex sample matrix, the bacterial biomass was purified using Accudenz gradient centrifugation (AGC) before protein extraction. The optimized 2DE method yielded high-quality gels suitable for quantitative comparative analysis and subsequent protein identification by LC-MS/MS. The optimized 2DE method could be adapted to other proteomic investigations involving MMC in complex organic or environmental matrices. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomic explorations of autism spectrum disorder.

Science.gov (United States)

Szoko, Nicholas; McShane, Adam J; Natowicz, Marvin R

2017-09-01

Proteomics, the large-scale study of protein expression in cells and tissues, is a powerful tool to study the biology of clinical conditions and has provided significant insights in many experimental systems. Herein, we review the basics of proteomic methodology and discuss challenges in using proteomic approaches to study autism. Unlike other experimental approaches, such as genomic approaches, there have been few large-scale studies of proteins in tissues from persons with autism. Most of the proteomic studies on autism used blood or other peripheral tissues; few studies used brain tissue. Some studies found dysregulation of aspects of the immune system or of aspects of lipid metabolism, but no consistent findings were noted. Based on the challenges in using proteomics to study autism, we discuss considerations for future studies. Apart from the complex technical considerations implicit in any proteomic analysis, key nontechnical matters include attention to subject and specimen inclusion/exclusion criteria, having adequate sample size to ensure appropriate powering of the study, attention to the state of specimens prior to proteomic analysis, and the use of a replicate set of specimens, when possible. We conclude by discussing some potentially productive uses of proteomics, potentially coupled with other approaches, for future autism research including: (1) proteomic analysis of banked human brain specimens; (2) proteomic analysis of tissues from animal models of autism; and (3) proteomic analysis of induced pluripotent stem cells that are differentiated into various types of brain cells and neural organoids. Autism Res 2017, 10: 1460-1469. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.

Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

Directory of Open Access Journals (Sweden)

Emmanuelle Maria Françoise Bayer

2013-01-01

Full Text Available In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma plays pivotal roles in the orchestration of development, defence responses and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialised domains of the endoplasmic reticulum and the plasma membrane. PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalisation or screening of random cDNAs, only few PD proteins had been conclusively identified and characterised. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on free PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD associated proteins.

Dissecting plasmodesmata molecular composition by mass spectrometry-based proteomics.

Science.gov (United States)

Salmon, Magali S; Bayer, Emmanuelle M F

2012-01-01

In plants, the intercellular communication through the membranous channels called plasmodesmata (PD; singular plasmodesma) plays pivotal roles in the orchestration of development, defence responses, and viral propagation. PD are dynamic structures embedded in the plant cell wall that are defined by specialized domains of the endoplasmic reticulum (ER) and the plasma membrane (PM). PD structure and unique functions are guaranteed by their particular molecular composition. Yet, up to recent years and despite numerous approaches such as mutant screens, immunolocalization, or screening of random cDNAs, only few PD proteins had been conclusively identified and characterized. A clear breakthrough in the search of PD constituents came from mass-spectrometry-based proteomic approaches coupled with subcellular fractionation strategies. Due to their position, firmly anchored in the extracellular matrix, PD are notoriously difficult to isolate for biochemical analysis. Proteomic-based approaches have therefore first relied on the use of cell wall fractions containing embedded PD then on "free" PD fractions whereby PD membranes were released from the walls by enzymatic degradation. To discriminate between likely contaminants and PD protein candidates, bioinformatics tools have often been used in combination with proteomic approaches. GFP fusion proteins of selected candidates have confirmed the PD association of several protein families. Here we review the accomplishments and limitations of the proteomic-based strategies to unravel the functional and structural complexity of PD. We also discuss the role of the identified PD-associated proteins.

Proteomics dataset

DEFF Research Database (Denmark)

Bennike, Tue Bjerg; Carlsen, Thomas Gelsing; Ellingsen, Torkell

2017-01-01

patients (Morgan et al., 2012; Abraham and Medzhitov, 2011; Bennike, 2014) [8–10. Therefore, we characterized the proteome of colon mucosa biopsies from 10 inflammatory bowel disease ulcerative colitis (UC) patients, 11 gastrointestinal healthy rheumatoid arthritis (RA) patients, and 10 controls. We...... been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001608 for ulcerative colitis and control samples, and PXD003082 for rheumatoid arthritis samples....

Ceramide binding to anandamide increases its half-life and potentiates its cytotoxicity in human neuroblastoma cells.

Science.gov (United States)

Di Scala, Coralie; Mazzarino, Morgane; Yahi, Nouara; Varini, Karine; Garmy, Nicolas; Fantini, Jacques; Chahinian, Henri

2017-06-01

Anandamide (AEA) is a ubiquitous lipid that exerts neurotransmitter functions but also controls important biological functions such as proliferation, survival, or programmed cell death. The latter effects are also regulated by ceramide, a lipid enzymatically generated from sphingomyelin hydrolysis by sphingomyelinase. Ceramide has been shown to increase the cellular toxicity of AEA, but the mechanisms controlling this potentiating effect remained unclear. Here we have used a panel of in silico, physicochemical, biochemical and cellular approaches to study the crosstalk between AEA and ceramide apoptotic pathways. Molecular dynamics simulations indicated that AEA and ceramide could form a stable complex in phosphatidylcholine membranes. Consistent with these data, we showed that AEA can specifically insert into ceramide monolayers whereas it did not penetrate into sphingomyelin membranes. Then we have studied the effects of ceramide on AEA-induced toxicity of human neuroblastoma cells. In these experiments, the cells have been either naturally enriched in ceramide by neutral sphingomyelinase pre-incubation or treated with C2-ceramide, a biologically active ceramide analog. Both treatments significantly increased the cytotoxicity of AEA as assessed by the MTS mitochondrial toxicity assay. This effect was correlated with the concomitant accumulation of natural ceramide (or its synthetic analog) and AEA in the cells. A kinetic study of AEA hydrolysis showed that ceramide inhibited the fatty acid amino hydrolase (FAAH) activity in cell extracts. Taken together, these data suggested that ceramide binds to AEA, increases its half-life and potentiates its cytotoxicity. Overall, these mechanisms account for a functional cross-talk between AEA and ceramide apoptotic pathways. Copyright © 2017 Elsevier B.V. All rights reserved.

The effective and environmental half-life of {sup 137}Cs at Coral Islands at the former US nuclear test site

Energy Technology Data Exchange (ETDEWEB)

Robison, William L. E-mail: robison1@llnl.gov; Conrado, Cynthia L.; Bogen, Kenneth T.; Stoker, A. Carol

2003-07-01

The United States (US) conducted nuclear weapons testing from 1946 to 1958 at Bikini and Enewetak Atolls in the northern Marshall Islands. Based on previous detailed dose assessments for Bikini, Enewetak, Rongelap, and Utirik Atolls over a period of 28 years, cesium-137 ({sup 137}Cs) at Bikini Atoll contributes about 85-89% of the total estimated dose through the terrestrial food chain as a result of uptake of {sup 137}Cs by food crops. The estimated integral 30, 50, and 70-year doses were based on the radiological decay of {sup 137}Cs (30-year half-life) and other radionuclides. However, there is a continuing inventory of {sup 137}Cs and {sup 90}Sr in the fresh water portion of the groundwater at all contaminated atolls even though the turnover rate of the fresh groundwater is about 5 years. This is evidence that a portion of the soluble fraction of {sup 137}Cs and {sup 90}Sr inventory in the soil is lost by transport to groundwater when rainfall is heavy enough to cause recharge of the lens, resulting in loss of {sup 137}Cs from the soil column and root zone of the plants. This loss is in addition to that caused by radioactive decay. The effective rate of loss was determined by two methods: (1) indirectly, from time-dependent studies of the {sup 137}Cs concentration in leaves of Pisonia grandis, Guettarda specosia, Tournefortia argentea (also called Messerschmidia), Scaevola taccada, and fruit from Pandanus and coconut trees (Cocos nucifera L.), and (2) more directly, by evaluating the {sup 137}Cs/{sup 90}Sr ratios at Bikini Atoll. The mean (and its lower and upper 95% confidence limits) for effective half-life and for environmental-loss half-life (ELH) based on all the trees studied on Rongelap, Bikini, and Enewetak Atolls are 8.5 years (8.0 years, 9.8 years), and 12 years (11 years, 15 years), respectively. The ELH based on the {sup 137}Cs/{sup 90}Sr ratios in soil in 1987 relative to the{sup 137}Cs/{sup 90}Sr ratios at the time of deposition in 1954 is less

A dynamic architecture of life [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Beatrix P. Rubin

2015-11-01

Full Text Available In recent decades, a profound conceptual transformation has occurred comprising different areas of biological research, leading to a novel understanding of life processes as much more dynamic and changeable. Discoveries in plants and animals, as well as novel experimental approaches, have prompted the research community to reconsider established concepts and paradigms. This development was taken as an incentive to organise a workshop in May 2014 at the Academia Nazionale dei Lincei in Rome. There, experts on epigenetics, regeneration, neuroplasticity, and computational biology, using different animal and plant models, presented their insights on important aspects of a dynamic architecture of life, which comprises all organisational levels of the organism. Their work demonstrates that a dynamic nature of life persists during the entire existence of the organism and permits animals and plants not only to fine-tune their response to particular environmental demands during development, but underlies their continuous capacity to do so. Here, a synthesis of the different findings and their relevance for biological thinking is presented.

Genomics, transcriptomics and proteomics to elucidate the pathogenesis of rheumatoid arthritis.

Science.gov (United States)

Song, Xinqiang; Lin, Qingsong

2017-08-01

Rheumatoid arthritis is an autoimmune disease that affects several organs and tissues, predominantly the synovial joints. The pathogenesis of this disease is not completely understood, which maybe involved in the genomic variations, gene expression, protein translation and post-translational modifications. These system variations in genomics, transcriptomics and proteomics are dynamic in nature and their crosstalk is overwhelmingly complex, thus analyzing them separately may not be very informative. However, various '-omics' techniques developed in recent years have opened up new possibilities for clarifying disease pathways and thereby facilitating early diagnosis and specific therapies. This review examines how recent advances in the fields of genomics, transcriptomics and proteomics have contributed to our understanding of rheumatoid arthritis.

Novel Pneumocystis Antigen Discovery Using Fungal Surface Proteomics

OpenAIRE

Zheng, Mingquan; Cai, Yang; Eddens, Taylor; Ricks, David M.; Kolls, Jay K.

2014-01-01

Pneumonia due to the fungus Pneumocystis jirovecii is a life-threatening infection that occurs in immunocompromised patients. The inability to culture the organism as well as the lack of an annotated genome has hindered antigen discovery that could be useful in developing novel vaccine- or antibody-based therapies as well as diagnostics for this infection. Here we report a novel method of surface proteomics analysis of Pneumocystis murina that reliably detected putative surface proteins that ...

Quantitative proteomic analysis of microdissected oral epithelium for cancer biomarker discovery.

Science.gov (United States)

Xiao, Hua; Langerman, Alexander; Zhang, Yan; Khalid, Omar; Hu, Shen; Cao, Cheng-Xi; Lingen, Mark W; Wong, David T W

2015-11-01

Specific biomarkers are urgently needed for the detection and progression of oral cancer. The objective of this study was to discover cancer biomarkers from oral epithelium through utilizing high throughput quantitative proteomics approaches. Morphologically malignant, epithelial dysplasia, and adjacent normal epithelial tissues were laser capture microdissected (LCM) from 19 patients and used for proteomics analysis. Total proteins from each group were extracted, digested and then labelled with corresponding isobaric tags for relative and absolute quantitation (iTRAQ). Labelled peptides from each sample were combined and analyzed by liquid chromatography-mass spectrometry (LC-MS/MS) for protein identification and quantification. In total, 500 proteins were identified and 425 of them were quantified. When compared with adjacent normal oral epithelium, 17 and 15 proteins were consistently up-regulated or down-regulated in malignant and epithelial dysplasia, respectively. Half of these candidate biomarkers were discovered for oral cancer for the first time. Cornulin was initially confirmed in tissue protein extracts and was further validated in tissue microarray. Its presence in the saliva of oral cancer patients was also explored. Myoglobin and S100A8 were pre-validated by tissue microarray. These data demonstrated that the proteomic biomarkers discovered through this strategy are potential targets for oral cancer detection and salivary diagnostics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Metabolically stable bradykinin B2 receptor agonists enhance transvascular drug delivery into malignant brain tumors by increasing drug half-life

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Glen Daniel

2009-05-01

-lysine-bradykinin and labradimil increased the blood half-life of Gd-DTPA sufficiently enough to increase significantly the tumor tissue Gd-DTPA area under the time-concentration curve. Conclusion Metabolically stable bradykinin B2 receptor agonists, methionine-lysine-bradykinin and labradimil, enhance the transvascular delivery of small chemotherapy drugs across the BBTB of malignant gliomas by increasing the blood half-life of the co-infused drug. The selectivity of the increase in drug delivery into the malignant glioma tissue, but not into normal brain tissue or skeletal muscle tissue, is due to the inherent porous nature of the BBTB of malignant glioma microvasculature.

Dynamic Path Analysis in Life-Course Epidemiology

DEFF Research Database (Denmark)

Gamborg, Michael Orland; Boje Jensen, Gorm; Sørensen, Thorkild I.A.

2011-01-01

it works through other risk factors. In this paper, the dynamic path analysis model is presented as a tool to analyze these dynamic mechanisms in life-course epidemiology. A key feature of dynamic path analysis is its ability to decompose the total effect of a risk factor into a direct effect (not mediated...... by other variables) and indirect effects (mediated through other variables). This is illustrated by examining the associations between repeated measurements of body mass index (BMI) and systolic blood pressure (SBP) and the risk of CHD in a sample of Danish men between 1976 and 2006. The effect of baseline...... BMI on the risk of CHD is decomposed into a direct effect and indirect effects going through later BMI, concurrent SBP, or later SBP. In conclusion, dynamic path analysis is a flexible tool that by the decomposition of effects can be used to increase the understanding of mechanisms that underlie...

1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions.

Science.gov (United States)

Joshi, Hiren J; Christiansen, Katy M; Fitz, Joffrey; Cao, Jun; Lipzen, Anna; Martin, Joel; Smith-Moritz, A Michelle; Pennacchio, Len A; Schackwitz, Wendy S; Weigel, Detlef; Heazlewood, Joshua L

2012-05-15

The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana. The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/

Development of CANDLES low background HPGe detector and half-life measurement of 180Tam

Science.gov (United States)

Chan, W. M.; Kishimoto, T.; Umehara, S.; Matsuoka, K.; Suzuki, K.; Yoshida, S.; Nakajima, K.; Iida, T.; Fushimi, K.; Nomachi, M.; Ogawa, I.; Tamagawa, Y.; Hazama, R.; Takemoto, Y.; Nakatani, N.; Takihira, Y.; Tozawa, M.; Kakubata, H.; Trang, V. T. T.; Ohata, T.; Tetsuno, K.; Maeda, T.; Khai, B. T.; Li, X. L.; Batpurev, T.

2018-01-01

A low background HPGe detector system was developed at CANDLES Experimental Hall for multipurpose use. Various low background techniques were employed, including hermatic shield design, radon gas suppression, and background reduction analysis. A new pulse shape discrimination (PSD) method was specially created for coaxial Ge detector. Using this PSD method, microphonics noise and background event at low energy region less than 200 keV can be rejected effectively. Monte Carlo simulation by GEANT4 was performed to acquire the detection efficiency and study the interaction of gamma-rays with detector system. For rare decay measurement, the detector was utilized to detect the nature's most stable isomer tantalum-180m (180Tam) decay. Two phases of tantalum physics run were completed with total livetime of 358.2 days, which Phase II has upgraded shield configuration. The world most stringent half-life limit of 180Tam has been successfully achieved.

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

Science.gov (United States)

Bryan, Kenneth; Jarboui, Mohamed-Ali; Raso, Cinzia; Bernal-Llinares, Manuel; McCann, Brendan; Rauch, Jens; Boldt, Karsten; Lynn, David J

2016-06-03

Recent advances in mass-spectrometry-based proteomics are now facilitating ambitious large-scale investigations of the spatial and temporal dynamics of the proteome; however, the increasing size and complexity of these data sets is overwhelming current downstream computational methods, specifically those that support the postquantification analysis pipeline. Here we present HiQuant, a novel application that enables the design and execution of a postquantification workflow, including common data-processing steps, such as assay normalization and grouping, and experimental replicate quality control and statistical analysis. HiQuant also enables the interpretation of results generated from large-scale data sets by supporting interactive heatmap analysis and also the direct export to Cytoscape and Gephi, two leading network analysis platforms. HiQuant may be run via a user-friendly graphical interface and also supports complete one-touch automation via a command-line mode. We evaluate HiQuant's performance by analyzing a large-scale, complex interactome mapping data set and demonstrate a 200-fold improvement in the execution time over current methods. We also demonstrate HiQuant's general utility by analyzing proteome-wide quantification data generated from both a large-scale public tyrosine kinase siRNA knock-down study and an in-house investigation into the temporal dynamics of the KSR1 and KSR2 interactomes. Download HiQuant, sample data sets, and supporting documentation at http://hiquant.primesdb.eu .

Normal Mode Analysis to a Poroelastic Half-Space Problem under Generalized Thermoelasticity

Directory of Open Access Journals (Sweden)

Chunbao Xiong

Full Text Available Abstract The thermo-hydro-mechanical problems associated with a poroelastic half-space soil medium with variable properties under generalized thermoelasticity theory were investigated in this study. By remaining faithful to Biot’s theory of dynamic poroelasticity, we idealized the foundation material as a uniform, fully saturated, poroelastic half-space medium. We first subjected this medium to time harmonic loads consisting of normal or thermal loads, then investigated the differences between the coupled thermohydro-mechanical dynamic models and the thermo-elastic dynamic models. We used normal mode analysis to solve the resulting non-dimensional coupled equations, then investigated the effects that non-dimensional vertical displacement, excess pore water pressure, vertical stress, and temperature distribution exerted on the poroelastic half-space medium and represented them graphically.

Measurements of half-lives of short-lived nuclides

International Nuclear Information System (INIS)

Elmali, A.

2001-01-01

In this work 19 F(n,p) 19 O (26.94 sec.), 76 Ge(n,2n) 75m Ge(47.73 sec.), 23 Na(n,p) 23 Ne (37.24 sec.) 23 Na(n,α) 20 F (11.12 sec.), 68 Zn(n,p) 68g Cu (31.11 sec.), 46 Ti(n,P) 46m Sc (18.70 sec.), 19 F(n,α) 16 N (7.13 sec.) and 92 Mo(n,2n) 91m Mo (65.40 sec.) half lives were determined. The half life measurements were performed utilizing the Sames T-400 neutron generator at the Physics Department of Cekmece Nuclear Research and Training Center, Istanbul. Fast neutrons (∼ 14 MeV) were produced via T(d,n)He reaction in a TIT target which was bombarded by 300 KeV deuterons. The samples bombarded with 14 MeV neutrons were transferred with a fast sample transport system from neutron source to the HPGe detector were the gamma measurements are performed. The time elapsed during the transport of the sample between the two stations were about 0.5 sec. in the experimental data, corrections were made for coincidence summing, pules pile up, dead time and background elimination. In order to test the accuracy and the sensitivity of the half-life measurement system used in this work, the 19 O half life form the 19 F(n,p) 19 O reaction were measured first and compared with the data given in a recently published JAERI report

Proteomic analysis of human tooth pulp: proteomics of human tooth.

Science.gov (United States)

Eckhardt, Adam; Jágr, Michal; Pataridis, Statis; Mikšík, Ivan

2014-12-01

The unique pulp-dentin complex demonstrates strong regenerative potential, which enables it to respond to disease and traumatic injury. Identifying the proteins of the pulp-dentin complex is crucial to understanding the mechanisms of regeneration, tissue calcification, defense processes, and the reparation of dentin by dental pulp. The lack of knowledge of these proteins limits the development of more efficient therapies. The proteomic profile of human tooth pulp was investigated and compared with the proteome of human dentin and blood. The samples of tooth pulp were obtained from 5 sound permanent human third molars of 5 adults (n = 5). The extracted proteins were separated by 2-dimensional gel electrophoresis, analyzed by nano-liquid chromatography tandem mass spectrometry, and identified by correlating mass spectra to the proteomic databases. A total of 342 proteins were identified with high confidence, and 2 proteins were detected for the first time in an actual human sample. The identified tooth pulp proteins have a variety of functions: structural, catalytic, transporter, protease activity, immune response, and many others. In a comparison with dentin and blood plasma, 140 (pulp/dentin) shared proteins were identified, 37 of which were not observed in plasma. It can be suggested that they might participate in the unique pulp-dentin complex. This proteomic investigation of human tooth pulp, together with the previously published study of human dentin, is one of the most comprehensive proteome lists of human teeth to date. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis.

Science.gov (United States)

Deng, Ning; Li, Zhenye; Pan, Chao; Duan, Huilong

2015-01-01

Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

Some problems of parametric neutron activation analysis based on the use of radioactive daughters of longer-lived mothers with low mother/daughter half-life ratios

International Nuclear Information System (INIS)

Cohen, I.M.

2012-01-01

The theoretical and practical aspects of the use of radioactive daughters originated from the decay of longer-lived radioactive mothers in parametric activation analysis, when the ratio: mother half-life to daughter half-life is less than 10, are discussed. The mother-daughter relationships: 47 Ca/ 47 Sc; 95 Zr/ 95 Nb; 140 Ba/ 140 La; 99 Mo/ 99m Tc and 115 Cd/ 115m In are selected as models for the study. The cases when the radionuclide of interest is formed through both direct and indirect routes are also analyzed. As illustrative example, the direct reaction and the reaction chain: 47 Ti(n,p) 47 Sc/ 46 Ca(n,γ) 47 Ca(β - ) 47 Sc are evaluated with respect to the determination of the elements involved and their reciprocal interferences. (author)

System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism

Directory of Open Access Journals (Sweden)

Lei Wang

2017-06-01

Full Text Available Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other

System-Level and Granger Network Analysis of Integrated Proteomic and Metabolomic Dynamics Identifies Key Points of Grape Berry Development at the Interface of Primary and Secondary Metabolism.

Science.gov (United States)

Wang, Lei; Sun, Xiaoliang; Weiszmann, Jakob; Weckwerth, Wolfram

2017-01-01

Grapevine is a fruit crop with worldwide economic importance. The grape berry undergoes complex biochemical changes from fruit set until ripening. This ripening process and production processes define the wine quality. Thus, a thorough understanding of berry ripening is crucial for the prediction of wine quality. For a systemic analysis of grape berry development we applied mass spectrometry based platforms to analyse the metabolome and proteome of Early Campbell at 12 stages covering major developmental phases. Primary metabolites involved in central carbon metabolism, such as sugars, organic acids and amino acids together with various bioactive secondary metabolites like flavonols, flavan-3-ols and anthocyanins were annotated and quantified. At the same time, the proteomic analysis revealed the protein dynamics of the developing grape berries. Multivariate statistical analysis of the integrated metabolomic and proteomic dataset revealed the growth trajectory and corresponding metabolites and proteins contributing most to the specific developmental process. K-means clustering analysis revealed 12 highly specific clusters of co-regulated metabolites and proteins. Granger causality network analysis allowed for the identification of time-shift correlations between metabolite-metabolite, protein- protein and protein-metabolite pairs which is especially interesting for the understanding of developmental processes. The integration of metabolite and protein dynamics with their corresponding biochemical pathways revealed an energy-linked metabolism before veraison with high abundances of amino acids and accumulation of organic acids, followed by protein and secondary metabolite synthesis. Anthocyanins were strongly accumulated after veraison whereas other flavonoids were in higher abundance at early developmental stages and decreased during the grape berry developmental processes. A comparison of the anthocyanin profile of Early Campbell to other cultivars revealed

Mining the granule proteome

DEFF Research Database (Denmark)

Albrethsen, Jakob; Goetze, Jens P; Johnsen, Anders H

2015-01-01

Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of g...

Total and spontaneous fission half-lives of the americium and curium nuclides

International Nuclear Information System (INIS)

Holden, N.E.

1984-01-01

The total half-life and the half-life for spontaneous fission are evaluated for the various long-lived nuclides of interest. Recommended values are presented for 241 Am, /sup 242m/Am, 243 Am, 242 Cm, 243 Cm, 244 Cm, 245 Cm, 246 Cm, 247 Cm, 248 Cm, and 250 Cm. The uncertainties are provided at the 95% confidence limit for each of the recommended values

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

Directory of Open Access Journals (Sweden)

Yalin Liao

2016-08-01

Full Text Available RNA functions through the dynamic formation of complexes with RNA-binding proteins (RBPs in all clades of life. We determined the RBP repertoire of beating cardiomyocytic HL-1 cells by jointly employing two in vivo proteomic methods, mRNA interactome capture and RBDmap. Together, these yielded 1,148 RBPs, 391 of which are shared with all other available mammalian RBP repertoires, while 393 are thus far unique to cardiomyocytes. RBDmap further identified 568 regions of RNA contact within 368 RBPs. The cardiomyocyte mRNA interactome composition reflects their unique biology. Proteins with roles in cardiovascular physiology or disease, mitochondrial function, and intermediary metabolism are all highly represented. Notably, we identified 73 metabolic enzymes as RBPs. RNA-enzyme contacts frequently involve Rossmann fold domains with examples in evidence of both, mutual exclusivity of, or compatibility between RNA binding and enzymatic function. Our findings raise the prospect of previously hidden RNA-mediated regulatory interactions among cardiomyocyte gene expression, physiology, and metabolism.

Advances of Proteomic Sciences in Dentistry.

Science.gov (United States)

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-05-13

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

Proteomics - new analytical approaches

International Nuclear Information System (INIS)

Hancock, W.S.

2001-01-01

Full text: Recent developments in the sequencing of the human genome have indicated that the number of coding gene sequences may be as few as 30,000. It is clear, however, that the complexity of the human species is dependent on the much greater diversity of the corresponding protein complement. Estimates of the diversity (discrete protein species) of the human proteome range from 200,000 to 300,000 at the lower end to 2,000,000 to 3,000,000 at the high end. In addition, proteomics (the study of the protein complement to the genome) has been subdivided into two main approaches. Global proteomics refers to a high throughput examination of the full protein set present in a cell under a given environmental condition. Focused proteomics refers to a more detailed study of a restricted set of proteins that are related to a specified biochemical pathway or subcellular structure. While many of the advances in proteomics will be based on the sequencing of the human genome, de novo characterization of protein microheterogeneity (glycosylation, phosphorylation and sulfation as well as the incorporation of lipid components) will be required in disease studies. To characterize these modifications it is necessary to digest the protein mixture with an enzyme to produce the corresponding mixture of peptides. In a process analogous to sequencing of the genome, shot-gun sequencing of the proteome is based on the characterization of the key fragments produced by such a digest. Thus, a glycopeptide and hence a specific glycosylation motif will be identified by a unique mass and then a diagnostic MS/MS spectrum. Mass spectrometry will be the preferred detector in these applications because of the unparalleled information content provided by one or more dimensions of mass measurement. In addition, highly efficient separation processes are an absolute requirement for advanced proteomic studies. For example, a combination of the orthogonal approaches, HPLC and HPCE, can be very powerful

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko

2017-05-10

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database.

Science.gov (United States)

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-06-23

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. The Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all predicted proteins from

Integration of gel-based and gel-free proteomic data for functional analysis of proteins through Soybean Proteome Database

KAUST Repository

Komatsu, Setsuko; Wang, Xin; Yin, Xiaojian; Nanjo, Yohei; Ohyanagi, Hajime; Sakata, Katsumi

2017-01-01

The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max ‘Enrei’). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique. Since 2015, the database has been expanded to incorporate data obtained by label-free mass spectrometry-based quantitative proteomics, which is a gel-free proteomic technique. Here, the portions of the database consisting of gel-free proteomic data are described. The gel-free proteomic database contains 39,212 proteins identified in 63 sample sets, such as temporal and organ-specific samples of soybean plants grown under flooding stress or non-stressed conditions. In addition, data on organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored. Furthermore, the database integrates multiple omics data such as genomics, transcriptomics, metabolomics, and proteomics. The SPD database is accessible at http://proteome.dc.affrc.go.jp/Soybean/. Biological significanceThe Soybean Proteome Database stores data obtained from both gel-based and gel-free proteomic techniques. The gel-free proteomic database comprises 39,212 proteins identified in 63 sample sets, such as different organs of soybean plants grown under flooding stress or non-stressed conditions in a time-dependent manner. In addition, organellar proteins identified in mitochondria, nuclei, and endoplasmic reticulum are stored in the gel-free proteomics database. A total of 44,704 proteins, including 5490 proteins identified using a gel-based proteomic technique, are stored in the SPD. It accounts for approximately 80% of all

Altered Proteomic Polymorphisms in the Caterpillar Body and Stroma of Natural Cordyceps sinensis during Maturation

Science.gov (United States)

Wu, Zi-Mei; Gao, Ling; Yao, Yi-Sang; Tan, Ning-Zhi; Wu, Jian-Yong; Ni, Luqun; Zhu, Jia-Shi

2014-01-01

Objective To examine the maturational changes in proteomic polymorphisms resulting from differential expression by multiple intrinsic fungi in the caterpillar body and stroma of natural Cordyceps sinensis (Cs), an integrated micro-ecosystem. Methods The surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) biochip technique was used to profile the altered protein compositions in the caterpillar body and stroma of Cs during its maturation. The MS chromatograms were analyzed using density-weighted algorithms to examine the similarities and cluster relationships among the proteomic polymorphisms of the Cs compartments and the mycelial products Hirsutella sinensis (Hs) and Paecilomyces hepiali (Ph). Results: SELDI-TOF MS chromatograms displayed dynamic proteomic polymorphism alterations among samples from the different Cs compartments during maturation. More than 1,900 protein bands were analyzed using density-weighted ZUNIX similarity equations and clustering methods, revealing integral polymorphism similarities of 57.4% between the premature and mature stromata and 42.8% between the premature and mature caterpillar bodies. The across-compartment similarity was low, ranging from 10.0% to 18.4%. Consequently, each Cs compartment (i.e., the stroma and caterpillar body) formed a clustering clade, and the 2 clades formed a Cs cluster. The polymorphic similarities ranged from 0.51% to 1.04% between Hs and the Cs compartments and were 2.8- to 4.8-fold higher (1.92%–4.34%) between Ph and the Cs compartments. The Hs and Ph mycelial samples formed isolated clades outside of the Cs cluster. Conclusion Proteomic polymorphisms in the caterpillar body and stroma of Cs change dynamically during maturation. The proteomic polymorphisms in Hs and Ph differ from those in Cs, suggesting the presence of multiple Cs-associated fungi and multiple Ophiocordyceps sinensis genotypes with altered differential protein expression in the Cs compartments

Prediction of thyroidal 131I effective half-life in patients with Graves' disease.

Science.gov (United States)

Zhang, Ruiguo; Zhang, Guizhi; Wang, Renfei; Tan, Jian; He, Yajing; Meng, Zhaowei

2017-10-06

Calculation of effective thyroidal half-life (Teff) of iodine-131( 131 I) is cumbersome and tedious. The aim of this study was to investigate factors that could be used to predict Teff and to develop a Teff prediction model in Graves' disease patients. A total of 256 patients with GD were involved in this study. We investigated the influences of age, gender, disease duration, thyroid weight, antithyroid drugs, antithyroid drugs discontinuation period (ADP), thyroid function indexes, thyroid autoantibodies, thyroid-stimulating hormone receptor antibody (TRAb) level and radioactive iodine uptake (RAIU) values before 131 I therapy on Teff, applying univariate and multivariate analyses. Teff correlated negatively with thyroid peroxidase antibody, TRAb and thyroid weight, as well as positively with 24-hour, 48-hour, and 72-hour RAIU. Additionally, a longer ADP (especially≥ 14d) or without antithyroid drugs before 131 I therapy led to a longer Teff. Stepwise multiple linear regression analysis showed that 24-hour and 72-hour RAIU were statistically significant predictors of Teff ( P Graves' disease, with high prediction accuracy.

Half-life Measurements of Levels in {sup 75}As

Energy Technology Data Exchange (ETDEWEB)

Hoejeberg, M; Malmskog, S G

1969-04-15

Half-lives for three levels in {sup 75}As have been determined using an electron-electron coincidence spectrometer. The following results have been obtained. T{sub 1/2} (199 keV) = 0.87 {+-} 0.03 nsec, T{sub 1/2} (280 keV) = 0.28 {+-} 0.02 nsec and T{sub 1/2} (401 keV) = 1. 67 {+-} 0.14 nsec.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius; Wong, Aloysius Tze; Groen, Arnoud; Serano, Natalia Lorena Gorron; Jankovic, Boris R.; Lilley, Kathryn; Gehring, Christoph A; Thomas, Ludivine

2014-01-01

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

Directory of Open Access Journals (Sweden)

Claudius Marondedze

2014-12-01

Full Text Available The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Exploring the Arabidopsis Proteome: Influence of Protein Solubilization Buffers on Proteome Coverage

KAUST Repository

Marondedze, Claudius

2014-12-31

The study of proteomes provides new insights into stimulus-specific responses of protein synthesis and turnover, and the role of post-translational modifications at the systems level. Due to the diverse chemical nature of proteins and shortcomings in the analytical techniques used in their study, only a partial display of the proteome is achieved in any study, and this holds particularly true for plant proteomes. Here we show that different solubilization and separation methods have profound effects on the resulting proteome. In particular, we observed that the type of detergents employed in the solubilization buffer preferentially enriches proteins in different functional categories. These include proteins with a role in signaling, transport, response to temperature stimuli and metabolism. This data may offer a functional bias on comparative analysis studies. In order to obtain a broader coverage, we propose a two-step solubilization protocol with first a detergent-free buffer and then a second step utilizing a combination of two detergents to solubilize proteins.

Proteomics and the Inner Ear

Directory of Open Access Journals (Sweden)

Isolde Thalmann

2001-01-01

Full Text Available The inner ear, one of the most complex organs, contains within its bony shell three sensory systems, the evolutionary oldest gravity receptor system, the three semicircular canals for the detection of angular acceleration, and the auditory system - unrivaled in sensitivity and frequency discrimination. All three systems are susceptible to a host of afflictions affecting the quality of life for all of us. In the first part of this review we present an introduction to the milestones of inner ear research to pave the way for understanding the complexities of a proteomics approach to the ear. Minute sensory structures, surrounded by large fluid spaces and a hard bony shell, pose extreme challenges to the ear researcher. In spite of these obstacles, a powerful preparatory technique was developed, whereby precisely defined microscopic tissue elements can be isolated and analyzed, while maintaining the biochemical state representative of the in vivo conditions. The second part consists of a discussion of proteomics as a tool in the elucidation of basic and pathologic mechanisms, diagnosis of disease, as well as treatment. Examples are the organ of Corti proteins OCP1 and OCP2, oncomodulin, a highly specific calcium-binding protein, and several disease entities, Meniere's disease, benign paroxysmal positional vertigo, and perilymphatic fistula.

Contribution of proteomics to the study of plant pathogenic fungi.

Science.gov (United States)

Gonzalez-Fernandez, Raquel; Jorrin-Novo, Jesus V

2012-01-01

Phytopathogenic fungi are one of the most damaging plant parasitic organisms, and can cause serious diseases and important yield losses in crops. The study of the biology of these microorganisms and the interaction with their hosts has experienced great advances in recent years due to the development of moderm, holistic and high-throughput -omic techniques, together with the increasing number of genome sequencing projects and the development of mutants and reverse genetics tools. We highlight among these -omic techniques the importance of proteomics, which has become a relevant tool in plant-fungus pathosystem research. Proteomics intends to identify gene products with a key role in pathogenicity and virulence. These studies would help in the search of key protein targets and in the development of agrochemicals, which may open new ways for crop disease diagnosis and protection. In this review, we made an overview on the contribution of proteomics to the knowledge of life cycle, infection mechanisms, and virulence of the plant pathogenic fungi. Data from current, innovative literature, according to both methodological and experimental systems, were summarized and discussed. Specific sections were devoted to the most studied fungal phytopathogens: Botrytis cinerea, Sclerotinia sclerotiorum, and Fusarium graminearum.

The Half-Half Plot

NARCIS (Netherlands)

Einmahl, J.H.J.; Gantner, M.

2009-01-01

The Half-Half (HH) plot is a new graphical method to investigate qualitatively the shape of a regression curve. The empirical HH-plot counts observations in the lower and upper quarter of a strip that moves horizontally over the scatter plot. The plot displays jumps clearly and reveals further

The half-half plot

NARCIS (Netherlands)

Einmahl, J.H.J.; Gantner, M.

2012-01-01

The Half-Half (HH) plot is a new graphical method to investigate qualitatively the shape of a regression curve. The empirical HH-plot counts observations in the lower and upper quarter of a strip that moves horizontally over the scatterplot. The plot displays jumps clearly and reveals further

Proteomic analysis of purified coronavirus infectious bronchitis virus particles

Directory of Open Access Journals (Sweden)

Shu Dingming

2010-06-01

Full Text Available Abstract Background Infectious bronchitis virus (IBV is the coronavirus of domestic chickens causing major economic losses to the poultry industry. Because of the complexity of the IBV life cycle and the small number of viral structural proteins, important virus-host relationships likely remain to be discovered. Toward this goal, we performed two-dimensional gel electrophoresis fractionation coupled to mass spectrometry identification approaches to perform a comprehensive proteomic analysis of purified IBV particles. Results Apart from the virus-encoded structural proteins, we detected 60 host proteins in the purified virions which can be grouped into several functional categories including intracellular trafficking proteins (20%, molecular chaperone (18%, macromolcular biosynthesis proteins (17%, cytoskeletal proteins (15%, signal transport proteins (15%, protein degradation (8%, chromosome associated proteins (2%, ribosomal proteins (2%, and other function proteins (3%. Interestingly, 21 of the total host proteins have not been reported to be present in virions of other virus families, such as major vault protein, TENP protein, ovalbumin, and scavenger receptor protein. Following identification of the host proteins by proteomic methods, the presence of 4 proteins in the purified IBV preparation was verified by western blotting and immunogold labeling detection. Conclusions The results present the first standard proteomic profile of IBV and may facilitate the understanding of the pathogenic mechanisms.

Estimating biodegradation half-lives for use in chemical screening.

Science.gov (United States)

Aronson, Dallas; Boethling, Robert; Howard, Philip; Stiteler, William

2006-06-01

Biodegradation half-lives are needed for many applications in chemical screening, but these data are not available for most chemicals. To address this, in phase one of this work we correlated the much more abundant ready and inherent biodegradation test data with measured half-lives for water and soil. In phase two, we explored the utility of the BIOWIN models (in EPI Suite) and molecular fragments for predicting half-lives. BIOWIN model output was correlated directly with measured half-lives, and new models were developed by re-regressing the BIOWIN fragments against the half-lives. All of these approaches gave the best results when used for binary (fast/slow) classification of half-lives, with accuracy generally in the 70-80% range. In the last phase, we used the collected half-life data to examine the default half-lives assigned by EPI Suite and the PBT Profiler for use as input to their level III multimedia models. It is concluded that estimated half-lives should not be used for purposes other than binning or prioritizing chemicals unless accuracy improves significantly.

Dynamic assessment for life extension of nuclear power plants (NPPs) using system dynamics (SD) method

International Nuclear Information System (INIS)

Woo, Tae Ho

2012-01-01

It has been proposed to extend the life of nuclear power plants (NPPs) for the economic purpose. Especially, the primary systems in reactor are considered in the thermohydraulic and neutronic aspect, which is related to the safety system. The electric power and the lifespan of components are expressed as economic situation. In addition, political considerations are given by the presidential change and the nuclear non-proliferation characteristics. The dynamical investigation using system dynamics (SD) shows the effective time for the life extension of the NPPs by Monte-Carlo simulations. This non-linear algorithm is incorporated with the feedback loop of the event sequences. The expected event is related to the past event, which affects to the dynamical simulations of lifetime in the NPPs. In the conclusions, the safety guarantee as well as the economic profit in the re-use of long term operated power plants is presented, which is mentioned as the transient time between 2019 and 2021 in this paper. (orig.)

Dynamic assessment for life extension of nuclear power plants (NPPs) using system dynamics (SD) method

Energy Technology Data Exchange (ETDEWEB)

Woo, Tae Ho [Seoul National Univ. (Korea, Republic of). Dept. of Nuclear Engineering

2012-12-15

It has been proposed to extend the life of nuclear power plants (NPPs) for the economic purpose. Especially, the primary systems in reactor are considered in the thermohydraulic and neutronic aspect, which is related to the safety system. The electric power and the lifespan of components are expressed as economic situation. In addition, political considerations are given by the presidential change and the nuclear non-proliferation characteristics. The dynamical investigation using system dynamics (SD) shows the effective time for the life extension of the NPPs by Monte-Carlo simulations. This non-linear algorithm is incorporated with the feedback loop of the event sequences. The expected event is related to the past event, which affects to the dynamical simulations of lifetime in the NPPs. In the conclusions, the safety guarantee as well as the economic profit in the re-use of long term operated power plants is presented, which is mentioned as the transient time between 2019 and 2021 in this paper. (orig.)

Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

Directory of Open Access Journals (Sweden)

Monica Soldi

2013-03-01

Full Text Available Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

Network-based analysis of proteomic profiles

KAUST Repository

Wong, Limsoon

2016-01-26

Mass spectrometry (MS)-based proteomics is a widely used and powerful tool for profiling systems-wide protein expression changes. It can be applied for various purposes, e.g. biomarker discovery in diseases and study of drug responses. Although RNA-based high-throughput methods have been useful in providing glimpses into the underlying molecular processes, the evidences they provide are indirect. Furthermore, RNA and corresponding protein levels have been known to have poor correlation. On the other hand, MS-based proteomics tend to have consistency issues (poor reproducibility and inter-sample agreement) and coverage issues (inability to detect the entire proteome) that need to be urgently addressed. In this talk, I will discuss how these issues can be addressed by proteomic profile analysis techniques that use biological networks (especially protein complexes) as the biological context. In particular, I will describe several techniques that we have been developing for network-based analysis of proteomics profile. And I will present evidence that these techniques are useful in identifying proteomics-profile analysis results that are more consistent, more reproducible, and more biologically coherent, and that these techniques allow expansion of the detected proteome to uncover and/or discover novel proteins.

Exploring the context of the lung proteome within the airway mucosa following allergen challenge.

Science.gov (United States)

Fehniger, Thomas E; Sato-Folatre, José-Gabriel; Malmström, Johan; Berglund, Magnus; Lindberg, Claes; Brange, Charlotte; Lindberg, Henrik; Marko-Varga, György

2004-01-01

The lung proteome is a dynamic collection of specialized proteins related to pulmonary function. Many cells of different derivations, activation states, and levels of maturity contribute to the changing environment, which produces the lung proteome. Inflammatory cells reacting to environmental challenge, for example from allergens, produce and secrete proteins which have profound effects on both resident and nonresident cells located in airways, alveoli, and the vascular tree which provides blood cells to the parenchyma alveolar bed for gas exchange. In an experimental model of allergic airway inflammation, we have compared control and allergen challenged lung compartments to determine global protein expression patterns using 2D-gel electrophoresis and subsequent spot identification by MS/MS mass spectrometry. We have then specifically isolated the epithelial mucosal layer, which lines conducting airways, from control and allergen challenged lungs, using laser capture technology and performed proteome identification on these selected cell samples. A central component of our investigations has been to contextually relate the histological features of the dynamic pulmonary environment to the changes in protein expression observed following challenge. Our results provide new information of the complexity of the submucosa/epithelium interface and the mechanisms behind the transformation of airway epithelium from normal steady states to functionally activated states.

Differential alkylation-based redox proteomics – Lessons learnt

Science.gov (United States)

Wojdyla, Katarzyna; Rogowska-Wrzesinska, Adelina

2015-01-01

Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S-sulfenylation are crucial mediators of intracellular redox signalling, with known associations to health and disease. Study of their functionalities has intensified thanks to the development of various analytical strategies, with particular contribution from differential alkylation-based proteomics methods. Presented here is a critical evaluation of differential alkylation-based strategies for the analysis of S-nitrosylation and S-sulfenylation. The aim is to assess the current status and to provide insights for future directions in the dynamically evolving field of redox proteomics. To achieve that we collected 35 original research articles published since 2010 and analysed them considering the following parameters, (i) resolution of modification site, (ii) quantitative information, including correction of modification levels by protein abundance changes and determination of modification site occupancy, (iii) throughput, including the amount of starting material required for analysis. The results of this meta-analysis are the core of this review, complemented by issues related to biological models and sample preparation in redox proteomics, including conditions for free thiol blocking and labelling of target cysteine oxoforms. PMID:26282677

Differential alkylation-based redox proteomics - Lessons learnt

DEFF Research Database (Denmark)

Wojdyla, Katarzyna; Rogowska-Wrzesinska, Adelina

2015-01-01

Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S-sulfenylati......Cysteine is one of the most reactive amino acids. This is due to the electronegativity of sulphur atom in the side chain of thiolate group. It results in cysteine being present in several distinct redox forms inside the cell. Amongst these, reversible oxidations, S-nitrosylation and S......-sulfenylation are crucial mediators of intracellular redox signalling, with known associations to health and disease. Study of their functionalities has intensified thanks to the development of various analytical strategies, with particular contribution from differential alkylation-based proteomics methods. Presented here...... is a critical evaluation of differential alkylation-based strategies for the analysis of S-nitrosylation and S-sulfenylation. The aim is to assess the current status and to provide insights for future directions in the dynamically evolving field of redox proteomics. To achieve that we collected 35 original...

Dynamical mean field study of the Mott transition in the half-filled Hubbard model on a triangular lattice

OpenAIRE

Aryanpour, K.; Pickett, W. E.; Scalettar, R. T.

2006-01-01

We employ dynamical mean field theory (DMFT) with a Quantum Monte Carlo (QMC) atomic solver to investigate the finite temperature Mott transition in the Hubbard model with the nearest neighbor hopping on a triangular lattice at half-filling. We estimate the value of the critical interaction to be $U_c=12.0 \\pm 0.5$ in units of the hopping amplitude $t$ through the evolution of the magnetic moment, spectral function, internal energy and specific heat as the interaction $U$ and temperature $T$ ...

KINETIC MODELLING AND HALF LIFE STUDY OF ADSORPTIVE BIOREMEDIATION OF SOIL ARTIFICIALLY CONTAMINATED WITH BONNY LIGHT CRUDE OIL

Directory of Open Access Journals (Sweden)

Samuel Enahoro Agarry

2015-06-01

Full Text Available In this study, comparative potential effects of commercial activated carbon (CAC and plantain peel-derived biochar (PPBC of different particle sizes and dosage to stimulate petroleum hydrocarbon biodegradation in soil were investigated. Microcosms containing soil were spiked with weathered Bonny light crude oil (WBLCO (10% w/w and amended with different particle sizes (0.02, 0.07 and 0.48 mm and dosage (20, 30 and 40 g of CAC and PPBC, respectively. The bioremediation experiments were carried out for a period of 28 days under laboratory conditions. The results showed that there was a positive relationship between the rate of petroleum hydrocarbons reduction and presence of the CAC and PPBC in crude oil contaminated soil microcosms. The WBLCO biodegradation data fitted well to the first-order kinetic model. The model revealed that WBLCO contaminated-soil microcosms amended with CAC and PPBC had higher biodegradation rate constants (k as well as lower half-life times (t1/2 than unamended soil (natural attenuation remediation system. The rate constants increased while half-life times decreased with decreased particle size and increased dosage of amendment agents. ANOVA statistical analysis revealed that WBLCO biodegradation in soil was significantly (p = 0.05 influenced by the addition of CAC and biochar amendment agents, respectively. However, Tukey’s post hoc test (at p = 0.05 showed that there was no significant difference in the bioremediation efficiency of CAC and PPBC. Thus, amendment of soils with biochar has the potential to be an inexpensive, efficient, environmentally friendly and relatively novel strategy to mitigate organic compound-contaminated soil.

Proteomics Insights into Autophagy.

Science.gov (United States)

Cudjoe, Emmanuel K; Saleh, Tareq; Hawkridge, Adam M; Gewirtz, David A

2017-10-01

Autophagy, a conserved cellular process by which cells recycle their contents either to maintain basal homeostasis or in response to external stimuli, has for the past two decades become one of the most studied physiological processes in cell biology. The 2016 Nobel Prize in Medicine and Biology awarded to Dr. Ohsumi Yoshinori, one of the first scientists to characterize this cellular mechanism, attests to its importance. The induction and consequent completion of the process of autophagy results in wide ranging changes to the cellular proteome as well as the secretome. MS-based proteomics affords the ability to measure, in an unbiased manner, the ubiquitous changes that occur when autophagy is initiated and progresses in the cell. The continuous improvements and advances in mass spectrometers, especially relating to ionization sources and detectors, coupled with advances in proteomics experimental design, has made it possible to study autophagy, among other process, in great detail. Innovative labeling strategies and protein separation techniques as well as complementary methods including immuno-capture/blotting/staining have been used in proteomics studies to provide more specific protein identification. In this review, we will discuss recent advances in proteomics studies focused on autophagy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intelligibility in microbial complex systems: Wittgenstein and the score of life.

Science.gov (United States)

Baquero, Fernando; Moya, Andrés

2012-01-01

Knowledge in microbiology is reaching an extreme level of diversification and complexity, which paradoxically results in a strong reduction in the intelligibility of microbial life. In our days, the "score of life" metaphor is more accurate to express the complexity of living systems than the classic "book of life." Music and life can be represented at lower hierarchical levels by music scores and genomic sequences, and such representations have a generational influence in the reproduction of music and life. If music can be considered as a representation of life, such representation remains as unthinkable as life itself. The analysis of scores and genomic sequences might provide mechanistic, phylogenetic, and evolutionary insights into music and life, but not about their real dynamics and nature, which is still maintained unthinkable, as was proposed by Wittgenstein. As complex systems, life or music is composed by thinkable and only showable parts, and a strategy of half-thinking, half-seeing is needed to expand knowledge. Complex models for complex systems, based on experiences on trans-hierarchical integrations, should be developed in order to provide a mixture of legibility and imageability of biological processes, which should lead to higher levels of intelligibility of microbial life.

Differential proteomics reveals the hallmarks of seed development in common bean (Phaseolus vulgaris L.)

NARCIS (Netherlands)

Parreira, J R; Bouraada, J; Fitzpatrick, M A; Silvestre, S; Bernardes da Silva, A; Marques da Silva, J; Almeida, A M; Fevereiro, P; Altelaar, A F M; Araújo, S S

2016-01-01

Common bean (Phaseolus vulgaris L.) is one of the most consumed staple foods worldwide. Little is known about the molecular mechanisms controlling seed development. This study aims to comprehensively describe proteome dynamics during seed development of common bean. A high-throughput gel-free

Dynamic Characterizations of an 8-frame, Half-Strip, High-speed X-ray Microchannel Plate Imager

International Nuclear Information System (INIS)

Ken Moy; Ming Wu; Craig Kruschwitz; Aric Tibbits; Matt Griffin; Greg Rochau

2008-01-01

High-speed microchannel plate (MCP)-based imagers are critical detectors for x-ray diagnostics employed on Z-experiments at Sandia National Laboratories (SNL) to measure time-resolved x-ray spectra and to image dynamic hohlraums. A multiframe design using eight half strips in one imager permits recordings of radiation events in discrete temporal snapshots to yield a time-evolved movie. We present data using various facilities to characterize the performance of this design. These characterization studies include DC and pulsed-voltage biased measurements in both saturated and linear operational regimes using an intense, short-pulsed UV laser. Electrical probe measurements taken to characterize the shape of the HV pulse propagating across the strips help to corroborate the spatial gain dependence

[Progress in stable isotope labeled quantitative proteomics methods].

Science.gov (United States)

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea.

Science.gov (United States)

Roy Chowdhury, Anindya; Dutta, Chitra

2012-06-12

Archaea evoke interest among researchers for two enigmatic characteristics -a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins) distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

A pursuit of lineage-specific and niche-specific proteome features in the world of archaea

Directory of Open Access Journals (Sweden)

Roy Chowdhury Anindya

2012-06-01

Full Text Available Abstract Background Archaea evoke interest among researchers for two enigmatic characteristics –a combination of bacterial and eukaryotic components in their molecular architectures and an enormous diversity in their life-style and metabolic capabilities. Despite considerable research efforts, lineage- specific/niche-specific molecular features of the whole archaeal world are yet to be fully unveiled. The study offers the first large-scale in silico proteome analysis of all archaeal species of known genome sequences with a special emphasis on methanogenic and sulphur-metabolising archaea. Results Overall amino acid usage in archaea is dominated by GC-bias. But the environmental factors like oxygen requirement or thermal adaptation seem to play important roles in selection of residues with no GC-bias at the codon level. All methanogens, irrespective of their thermal/salt adaptation, show higher usage of Cys and have relatively acidic proteomes, while the proteomes of sulphur-metabolisers have higher aromaticity and more positive charges. Despite of exhibiting thermophilic life-style, korarchaeota possesses an acidic proteome. Among the distinct trends prevailing in COGs (Cluster of Orthologous Groups of proteins distribution profiles, crenarchaeal organisms display higher intra-order variations in COGs repertoire, especially in the metabolic ones, as compared to euryarchaea. All methanogens are characterised by a presence of 22 exclusive COGs. Conclusions Divergences in amino acid usage, aromaticity/charge profiles and COG repertoire among methanogens and sulphur-metabolisers, aerobic and anaerobic archaea or korarchaeota and nanoarchaeota, as elucidated in the present study, point towards the presence of distinct molecular strategies for niche specialization in the archaeal world.

Typology of Regions by Level and Dynamics of the Quality of Life

Directory of Open Access Journals (Sweden)

Boris Mikhailovich Grinchel’

2015-07-01

Full Text Available The paper considers the methodology and algorithm for the construction of typologies of regions in a two-dimensional space “level of development – dynamics of development” taking into account the quality of life, which is one of the most relevant competitiveness factors at the present stage of Russia’s development. The authors analyze the concept of “quality of life” and propose their own variant of the concept, on the basis of which they make a list of indicators for measuring and assessing the “quality of life” factor. In the implementation of the algorithm it is proposed to transform specific indicators, which assess the level and dynamics of the quality of life, into nonmetric numerical scores, normalized to the weighted average values of indicators for the Russian regions. The method of transformation of indicators into scores was tested on the example of the Northwestern Federal District regions, and the typologies in a two-dimensional space “level – dynamics” of the quality of life were made for 80 regions of Russia; the level of the quality of life was assessed according to official statistics for 2013, and the dynamics of the quality of life was assessed with the use of official statistics for 2011–2013. A detailed analysis is provided for each of the proposed typological groups and characteristics of this typology are highlighted. The proposed methodology and algorithm make it possible to compare and analyze not only the level and dynamics of development of different factors promoting competitive attractiveness, but also the interaction b etween the factors, for example, such as economy and the quality of life, economy and innovation, innovation and human resources, quality of life and innovation, etc. The typology provides a better understanding of advantages and disadvantages of both federal and local social policy for regional strategic development and helps justify the need and the focus of territorial

NIH Common Fund - Disruptive Proteomics Technologies - Challenges and Opportunities | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

This Request for Information (RFI) is directed toward determining how best to accelerate research in disruptive proteomics technologies. The Disruptive Proteomics Technologies (DPT) Working Group of the NIH Common Fund wishes to identify gaps and opportunities in current technologies and methodologies related to proteome-wide measurements.  For the purposes of this RFI, “disruptive” is defined as very rapid, very significant gains, similar to the "disruptive" technology development that occurred in DNA sequencing technology.

A decade of proteomics accomplished! Central and Eastern European Proteomic Conference (CEEPC) celebrates its 10th Anniversary in Budapest, Hungary.

Science.gov (United States)

Gadher, Suresh Jivan; Drahos, László; Vékey, Károly; Kovarova, Hana

2017-07-01

The Central and Eastern European Proteomic Conference (CEEPC) proudly celebrated its 10th Anniversary with an exciting scientific program inclusive of proteome, proteomics and systems biology in Budapest, Hungary. Since 2007, CEEPC has represented 'state-of the-art' proteomics in and around Central and Eastern Europe and these series of conferences have become a well-recognized event in the proteomic calendar. Fresher challenges and global healthcare issues such as ageing and chronic diseases are driving clinical and scientific research towards regenerative, reparative and personalized medicine. To this end, proteomics may enable diverse intertwining research fields to reach their end goals. CEEPC will endeavor to facilitate these goals.

Proteome alteration induced by hTERT transfection of human fibroblast cells.

Science.gov (United States)

Mazzucchelli, Gabriel D; Gabelica, Valérie; Smargiasso, Nicolas; Fléron, Maximilien; Ashimwe, Wilson; Rosu, Frédéric; De Pauw-Gillet, Marie-Claire; Riou, Jean-François; De Pauw, Edwin

2008-04-17

Telomerase confers cellular immortality by elongating telomeres, thereby circumventing the Hayflick limit. Extended-life-span cells have been generated by transfection with the human telomerase reverse transcriptase (hTERT) gene. hTERT transfected cell lines may be of outstanding interest to monitor the effect of drugs targeting the telomerase activity. The incidence of hTERT gene transfection at the proteome level is a prerequisite to that purpose. The effect of the transfection has been studied on the proteome of human fibroblast (WI38). Cytosolic and nuclear fractions of WI38 cells, empty vector transfected WI38 (WI38-HPV) and hTERT WI38 cells were submitted to a 2D-DIGE (Two-Dimensional Differential In-Gel Electrophoresis) analysis. Only spots that had a similar abundance in WI38 and WI38-HPV, but were differentially expressed in WI38 hTERT were selected for MS identification. This method directly points to the proteins linked with the hTERT expression. Number of false positive differentially expressed proteins has been excluded by using control WI38-HPV cells. The proteome alteration induced by hTERT WI38 transfection should be taken into account in subsequent use of the cell line for anti-telomerase drugs evaluation. 2D-DIGE experiment shows that 57 spots out of 2246 are significantly differentially expressed in the cytosolic fraction due to hTERT transfection, and 38 were confidently identified. In the nuclear fraction, 44 spots out of 2172 were selected in the differential proteome analysis, and 14 were identified. The results show that, in addition to elongating telomeres, hTERT gene transfection has other physiological roles, among which an enhanced ER capacity and a potent cell protection against apoptosis. We show that the methodology reduces the complexity of the proteome analysis and highlights proteins implicated in other processes than telomere elongation. hTERT induced proteome changes suggest that telomerase expression enhances natural cell repair

Proteome alteration induced by hTERT transfection of human fibroblast cells

Directory of Open Access Journals (Sweden)

Riou Jean-François

2008-04-01

Full Text Available Abstract Background Telomerase confers cellular immortality by elongating telomeres, thereby circumventing the Hayflick limit. Extended-life-span cells have been generated by transfection with the human telomerase reverse transcriptase (hTERT gene. hTERT transfected cell lines may be of outstanding interest to monitor the effect of drugs targeting the telomerase activity. The incidence of hTERT gene transfection at the proteome level is a prerequisite to that purpose. The effect of the transfection has been studied on the proteome of human fibroblast (WI38. Cytosolic and nuclear fractions of WI38 cells, empty vector transfected WI38 (WI38-HPV and hTERT WI38 cells were submitted to a 2D-DIGE (Two-Dimensional Differential In-Gel Electrophoresis analysis. Only spots that had a similar abundance in WI38 and WI38-HPV, but were differentially expressed in WI38 hTERT were selected for MS identification. This method directly points to the proteins linked with the hTERT expression. Number of false positive differentially expressed proteins has been excluded by using control WI38-HPV cells. The proteome alteration induced by hTERT WI38 transfection should be taken into account in subsequent use of the cell line for anti-telomerase drugs evaluation. Results 2D-DIGE experiment shows that 57 spots out of 2246 are significantly differentially expressed in the cytosolic fraction due to hTERT transfection, and 38 were confidently identified. In the nuclear fraction, 44 spots out of 2172 were selected in the differential proteome analysis, and 14 were identified. The results show that, in addition to elongating telomeres, hTERT gene transfection has other physiological roles, among which an enhanced ER capacity and a potent cell protection against apoptosis. Conclusion We show that the methodology reduces the complexity of the proteome analysis and highlights proteins implicated in other processes than telomere elongation. hTERT induced proteome changes suggest

Recent mass spectrometry-based proteomics for biomarker discovery in lung cancer, COPD, and asthma.

Science.gov (United States)

Fujii, Kiyonaga; Nakamura, Haruhiko; Nishimura, Toshihide

2017-04-01

Lung cancer and related diseases have been one of the most common causes of deaths worldwide. Genomic-based biomarkers may hardly reflect the underlying dynamic molecular mechanism of functional protein interactions, which is the center of a disease. Recent developments in mass spectrometry (MS) have made it possible to analyze disease-relevant proteins expressed in clinical specimens by proteomic challenges. Areas covered: To understand the molecular mechanisms of lung cancer and its subtypes, chronic obstructive pulmonary disease (COPD), asthma and others, great efforts have been taken to identify numerous relevant proteins by MS-based clinical proteomic approaches. Since lung cancer is a multifactorial disease that is biologically associated with asthma and COPD among various lung diseases, this study focused on proteomic studies on biomarker discovery using various clinical specimens for lung cancer, COPD, and asthma. Expert commentary: MS-based exploratory proteomics utilizing clinical specimens, which can incorporate both experimental and bioinformatic analysis of protein-protein interaction and also can adopt proteogenomic approaches, makes it possible to reveal molecular networks that are relevant to a disease subgroup and that could differentiate between drug responders and non-responders, good and poor prognoses, drug resistance, and so on.

Proteome reference map of Drosophila melanogaster head.

Science.gov (United States)

Lee, Tian-Ren; Huang, Shun-Hong; Lee, Chi-Ching; Lee, Hsiao-Yun; Chan, Hsin-Tzu; Lin, Kuo-Sen; Chan, Hong-Lin; Lyu, Ping-Chiang

2012-06-01

Drosophila melanogaster has been used as a genetic model organism to understand the fundamental molecular mechanisms in human biology including memory formation that has been reported involving protein synthesis and/or post-translational modification. In this study, we employed a proteomic platform based on fluorescent 2DE and MALDI-TOF MS to build a standard D. melanogaster head proteome map for proteome-proteome comparison. In order to facilitate the comparison, an interactive database has been constructed for systematically integrating and analyzing the proteomes from different conditions and further implicated to study human diseases related to D. melanogaster model. In summary, the fundamental head proteomic database and bioinformatic analysis will be useful for further elucidating the biological mechanisms such as memory formation and neurodegenerative diseases. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea

KAUST Repository

Chandramouli, Kondethimmanahalli

2015-12-15

Background The barnacle Balanus amphitrite is widely distributed in marine shallow and tidal waters, and has significant economic and ecological importance. Nauplii, the first larval stage of most crustaceans, are extremely abundant in the marine zooplankton. However, a lack of genome information has hindered elucidation of the molecular mechanisms of development, settlement and survival strategies in extreme marine environments. We sequenced and constructed the genome dataset for nauplii to obtain comprehensive larval genetic information. We also investigated iTRAQ-based protein expression patterns to reveal the molecular basis of nauplii development, and to gain information on larval survival strategies in the Red Sea marine environment. Results A nauplii larval transcript dataset, containing 92,117 predicted open reading frames (ORFs), was constructed and used as a reference for the proteome analysis. Genes related to translation, oxidative phosphorylation and cytoskeletal development were highly abundant. We observed remarkable plasticity in the proteome of Red Sea larvae. The proteins associated with development, stress responses and osmoregulation showed the most significant differences between the two larval populations studied. The synergistic overexpression of heat shock and osmoregulatory proteins may facilitate larval survival in intertidal habitats or in extreme environments. Conclusions We presented, for the first time, comprehensive transcriptome and proteome datasets for Red Sea nauplii. The datasets provide a foundation for future investigations focused on the survival mechanisms of other crustaceans in extreme marine environments.

Mapping of Proteomic Composition on the Surfaces of Bacillus spores by Atomic Force Microscopy-based Immunolabeling

Energy Technology Data Exchange (ETDEWEB)

Plomp, M; Malkin, A J

2008-06-02

Atomic force microscopy provides a unique capability to image high-resolution architecture and structural dynamics of pathogens (e.g. viruses, bacteria and bacterial spores) at near molecular resolution in native conditions. Further development of atomic force microscopy in order to enable the correlation of pathogen protein surface structures with specific gene products is essential to understand the mechanisms of the pathogen life cycle. We have applied an AFM-based immunolabeling technique for the proteomic mapping of macromolecular structures through the visualization of the binding of antibodies, conjugated with nanogold particles, to specific epitopes on Bacillus spore surfaces. This information is generated while simultaneously acquiring the surface morphology of the pathogen. The immunospecificity of this labeling method was established through the utilization of specific polyclonal and monoclonal antibodies that target spore coat and exosporium epitopes of Bacillus atrophaeus and Bacillus anthracis spores.

Half-life and mass measurement of the short-lived {sup 215}Po isotope (1.78 ms) at the FRS ion catcher

Energy Technology Data Exchange (ETDEWEB)

Rink, Ann-Kathrin; Bergmann, Julian; Ebert, Jens; Hornung, Christine; Miskun, Ivan; Reiter, Moritz P. [Justus-Liebig Universitaet Giessen (Germany); Ayet San Andres, Samuel; Dickel, Timo; Plass, Wolfgang R.; Scheidenberger, Christoph [Justus-Liebig Universitaet Giessen (Germany); GSI, Darmstadt (Germany); Geissel, Hans; Purushothaman, Sivaji [GSI, Darmstadt (Germany)

2016-07-01

At the Low-Energy Branch (LEB) of the Super-FRS at FAIR, precision experiments with exotic nuclei will be performed using ion traps and lasers. The nuclei will be produced at relativistic energies, slowed down, thermalised in a cryogenic stopping cell (CSC) and made available to various experiments. The thermalisation is a challenging task because of the large energy straggling of the nuclei after production, which requires a stopping cell with large areal densities. Also, the process needs to be performed on a millisecond time scale in order to give access to short-lived nuclides. This method has already been successfully applied at the FRS Ion Catcher at GSI using a prototype CSC. Recently the potential of the method has been demonstrated by the mass and half-life measurement of the {sup 215}Po nuclide with a half-life of 1.78 ms only. The multiple-reflection time-of-flight mass spectrometer at the FRS Ion Catcher has been used to determine the mass to a sub-ppm accuracy and to provide a mass-selected beam for alpha spectroscopy. Furthermore, experiments have been performed with the prototype CSC in order to test novel concepts to be used with the final version of the CSC for the LEB.

Half-lives of cluster decay of neutron rich nuclei in trans-tin region

International Nuclear Information System (INIS)

Swamy, G.S.; Umesh, T.K.

2011-01-01

In this work, the logarithmic half-life [log 10 (T 1/2 )] values have been reported for the exotic decay of some neutron rich even–even parent nuclei (56≤Z≤64) accompanied by the emission of alpha-like and non-alpha-like clusters in the trans-tin region. These values were calculated by using the single line of universal curve (UNIV) for alpha and cluster radioactive decay as well as the universal decay law (UDL). The half-life values were also separately calculated by considering the interacting nuclear potential barrier as the sum of Coulomb and proximity potentials. The half-life values based on the three calculations mentioned above, were found to agree with one another within a few orders of magnitude. Possible conclusions are drawn based on the present study. (author)

Proteomics in pulmonary research: selected methodical aspects

Directory of Open Access Journals (Sweden)

Martin Petrek

2007-10-01

Full Text Available Recent years witness rapid expansion of applications of proteomics to clinical research including non-malignant lung disorders. These developments bring along the need for standardisation of proteomic experiments. This paper briefly reviews basic methodical aspects of appliedproteomic studies using SELDI-TOF mass spectrometry platform as example but also emphasizes general aspects of quality assurance in proteomics. Key-words: lung proteome, quality assurance, SELDI-TOF MS

The potato tuber mitochondrial proteome

DEFF Research Database (Denmark)

Salvato, Fernanda; Havelund, Jesper Foged; Chen, Mingjie

2014-01-01

Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum 'Folva') and their proteome investigated. Proteins...... manner using normalized spectral counts including as many as 5-fold more "extreme" proteins (low mass, high isoelectric point, hydrophobic) than previous mitochondrial proteome studies. We estimate that this compendium of proteins represents a high coverage of the potato tuber mitochondrial proteome...

Ubiquitination dynamics in the early-branching eukaryote Giardia intestinalis

Science.gov (United States)

Niño, Carlos A; Chaparro, Jenny; Soffientini, Paolo; Polo, Simona; Wasserman, Moises

2013-01-01

Ubiquitination is a highly dynamic and versatile posttranslational modification that regulates protein function, stability, and interactions. To investigate the roles of ubiquitination in a primitive eukaryotic lineage, we utilized the early-branching eukaryote Giardia intestinalis. Using a combination of biochemical, immunofluorescence-based, and proteomics approaches, we assessed the ubiquitination status during the process of differentiation in Giardia. We observed that different types of ubiquitin modifications present specific cellular and temporal distribution throughout the Giardia life cycle from trophozoites to cyst maturation. Ubiquitin signal was detected in the wall of mature cysts, and enzymes implicated in cyst wall biogenesis were identified as substrates for ubiquitination. Interestingly, inhibition of proteasome activity did not affect trophozoite replication and differentiation, while it caused a decrease in cyst viability, arguing for proteasome involvement in cyst wall maturation. Using a proteomics approach, we identified around 200 high-confidence ubiquitinated candidates that vary their ubiquitination status during differentiation. Our results indicate that ubiquitination is critical for several cellular processes in this primitive eukaryote. PMID:23613346

Ecological half-life of 137Cs in plants associated with a contaminated stream

International Nuclear Information System (INIS)

Peles, John D.; Smith, Michael H.; Lehr Brisbin, I.

2002-01-01

Ecological half-life (T e ) is a useful measure for studying the long-term decline of contaminants, such as radionuclides, in natural systems. The current investigation determined levels of radiocesium ( 137 Cs) in two aquatic (Polygonum punctatum, Sagittaria latifolia) and three terrestrial (Alnus serrulata, Myrica cerifera, Salix nigra) plant species from a contaminated stream and floodplain on the U.S. Department of Energy's Savannah River Site. Current 137 Cs levels in plants were used in conjunction with historical data to determine T e of 137 Cs in each species. Median concentrations of 137 Cs were highest in S. latifolia (0.84 Bq g -1 ) and lowest in M. cerifera (0.10 Bq g -1 ). T e 's ranged from 4.85 yr in M. cerifera to 8.35 yr in S. nigra, both terrestrial species. T e 's for all aquatic (6.30 yr) and all terrestrial (5.87) species combined were very similar. The T e 's of the two aquatic primary producers (P. punctatum and S. latifolia) in the Steel Creek ecosystem were somewhat longer than T e values previously reported for some consumers from this ecosystem

Half-lives of 132La and 135La

Science.gov (United States)

Abel, E. P.; Clause, H. K.; Fonslet, J.; Nickles, R. J.; Severin, G. W.

2018-03-01

The half-lives of 135La and 132La were determined via serial gamma spectroscopy, and the half-life of 135La was further determined by a high-precision ionization-chamber measurement. The results are 18.91(2) hr for 135La and 4.59(4) hr for 132La compared with the previously compiled values of 19.5(2) hr and 4.8(2) hr, respectively. These lanthanum isotopes comprise a medically interesting system with positron emitter 132La and Auger-electron emitter 135La forming a theranostic pair for internal diagnostics and therapeutics. The precise half-lives are necessary for proper evaluation of their value in medicine and for a more representative tabulation of nuclear data.

The half-lives of biological activity of some pesticides in water

OpenAIRE

Kyaw Myint Oo,

2001-01-01

In the absence of analytical methods, the half-lives of biological activity of pesticides can be estimated by bioassays. To determine the half-lives of biological acivity of pesticides to fish, static bioassays were conducted in the laboratory with ten different formulations of pesticides using Labeo rohita as a bio-indicator. The half-lives of biological activity for ten different pesticides in soft water at pH 7.5 and 27░C, ranged from 4.6 days to 11.8 days. The half-life of biological acti...

Theoretical studies on the α decay half-lives of hyper and normal ...

Indian Academy of Sciences (India)

The α decay half-lives of hyper and normal isotopes of Po nuclei are studied in the present work. The inclusion of Λ – N interaction changes the half-life for α decay. The theoretical predictions on the α decay half-lives of normal Po isotopes are compared with experimental results and are seen to be matching well with each ...

Targeted proteomics guided by label-free global proteome analysis in saliva reveal transition signatures from health to periodontal disease.

Science.gov (United States)

Bostanci, Nagihan; Selevsek, Nathalie; Wolski, Witold; Grossmann, Jonas; Bao, Kai; Wahlander, Asa; Trachsel, Christian; Schlapbach, Ralph; Özturk, Veli Özgen; Afacan, Beral; Emingil, Gulnur; Belibasakis, Georgios N

2018-04-02

Periodontal diseases are among the most prevalent worldwide, but largely silent, chronic diseases. They affect the tooth-supporting tissues with multiple ramifications on life quality. Their early diagnosis is still challenging, due to lack of appropriate molecular diagnostic methods. Saliva offers a non-invasively collectable reservoir of clinically relevant biomarkers, which, if utilized efficiently, could facilitate early diagnosis and monitoring of ongoing disease. Despite several novel protein markers being recently enlisted by discovery proteomics, their routine diagnostic application is hampered by the lack of validation platforms that allow for rapid, accurate and simultaneous quantification of multiple proteins in large cohorts. We carried out a pipeline of two proteomic platforms; firstly, we applied open ended label-free quantitative (LFQ) proteomics for discovery in saliva (n=67, health, gingivitis, and periodontitis), followed by selected-reaction monitoring (SRM)-targeted proteomics for validation in an independent cohort (n=82). The LFQ platform led to the discovery of 119 proteins with at least two-fold significant difference between health and disease. The 65 proteins chosen for the subsequent SRM platform included 50 related proteins derived from the significantly enriched processes of the LFQ data, 11 from literature-mining, and four house-keeping ones. Among those, 60 were reproducibly quantifiable proteins (92% success rate), represented by a total of 143 peptides. Machine-learning modeling led to a narrowed-down panel of five proteins of high predictive value for periodontal diseases (higher in disease: Matrix metalloproteinase-9, Ras-related protein-1, Actin-related protein 2/3 complex subunit 5; lower in disease: Clusterin, Deleted in Malignant Brain Tumors 1), with maximum area under the receiver operating curve >0.97. This panel enriches the pool of credible clinical biomarker candidates for diagnostic assay development. Yet, the quantum

Dynamics of mathematical models in biology bringing mathematics to life

CERN Document Server

Zazzu, Valeria; Guarracino, Mario

2016-01-01

This volume focuses on contributions from both the mathematics and life science community surrounding the concepts of time and dynamicity of nature, two significant elements which are often overlooked in modeling process to avoid exponential computations. The book is divided into three distinct parts: dynamics of genomes and genetic variation, dynamics of motifs, and dynamics of biological networks. Chapters included in dynamics of genomes and genetic variation analyze the molecular mechanisms and evolutionary processes that shape the structure and function of genomes and those that govern genome dynamics. The dynamics of motifs portion of the volume provides an overview of current methods for motif searching in DNA, RNA and proteins, a key process to discover emergent properties of cells, tissues, and organisms. The part devoted to the dynamics of biological networks covers networks aptly discusses networks in complex biological functions and activities that interpret processes in cells. Moreover, chapters i...

Dynamics and life histories of northern ungulates in changing environments

Science.gov (United States)

Hendrichsen, D. K.

2011-12-01

Regional climate and local weather conditions can profoundly influence life history parameters (growth, survival, fecundity) and population dynamics in northern ungulates (Post and Stenseth 1999, Coulson et al. 2001). The influence is both direct, for example through reduced growth or survival (Aanes et al. 2000, Tyler et al. 2008), and indirect, for example through changes in resource distribution, phenology and quality, changes which subsequently influence consumer dynamics (Post et al. 2008). By comparing and contrasting data from three spatially independent populations of ungulates, I discuss how variation in local weather parameters and vegetation growth influence spatial and temporal dynamics through changes in life history parameters and/or behavioural dynamics. The data originate from long term (11-15 years) monitoring data from three populations of ungulates in one subarctic and two high Arctic sites; semi-domesticated reindeer (Rangifer tarandus tarandus) in northern Norway, Svalbard reindeer (R. t. platyrhynchus) on Spitsbergen and muskoxen (Ovibos moschatus) in Northeast Greenland. The results show that juvenile animals can be particularly vulnerable to changes in their environment, and that this is mirrored to different degrees in the spatio-temporal dynamics of the three populations. Adverse weather conditions, acting either directly or mediated through access to and quality of vegetation, experienced by young early in life, or even by their dams during pregnancy, can lead to reduced growth, lower survival and reduced reproductive performance later in life. The influence of current climatic variation, and the predictions of how local weather conditions may change over time, differs between the three sites, resulting in potentially different responses in the three populations. Aanes R, Saether BE and Øritsland NA. 2000. Fluctuations of an introduced population of Svalbard reindeer: the effects of density dependence and climatic variation. Ecography

New systematics of cluster- and alpha-decay half lives

International Nuclear Information System (INIS)

Poenaru, D.N.; Greiner, W.

1994-01-01

Available as short communication only. The cluster (or 'exotic') radioactivities belong to a rich variety of nuclear decay modes which are phenomena intermediate between fission and alpha decay. In this contribution a single universal curve for the logarithm of the partial half-life for each kind of cluster radioactivity of even-even parent nuclei is presented. This handy relationship reproduces well the up to now 14 even-even half-life measurements within a ratio of 3.86 or rms=0.587 orders of magnitude. Its universality consists in the fact that instead of having different lines for various parent nuclei, like in the 'classical' systematics (Geiger-Nuttall plot) one can get practically only one line for each decay mode. (Author) 1 Fig., 2 Refs

Proteomic Analysis of Chinese Hamster Ovary Cells

DEFF Research Database (Denmark)

Baycin-Hizal, Deniz; Tabb, David L.; Chaerkady, Raghothama

2012-01-01

To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis, multidimens......To complement the recent genomic sequencing of Chinese hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells including the cellular proteome, secretome, and glycoproteome using tandem mass spectrometry (MS/MS) of multiple fractions obtained from gel electrophoresis...

Independent Analysis of the Flagellum Surface and Matrix Proteomes Provides Insight into Flagellum Signaling in Mammalian-infectious Trypanosoma brucei*

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Oberholzer, Michael; Langousis, Gerasimos; Nguyen, HoangKim T.; Saada, Edwin A.; Shimogawa, Michelle M.; Jonsson, Zophonias O.; Nguyen, Steven M.; Wohlschlegel, James A.; Hill, Kent L.

2011-01-01

The flagellum of African trypanosomes is an essential and multifunctional organelle that functions in motility, cell morphogenesis, and host-parasite interaction. Previous studies of the trypanosome flagellum have been limited by the inability to purify flagella without first removing the flagellar membrane. This limitation is particularly relevant in the context of studying flagellum signaling, as signaling requires surface-exposed proteins in the flagellar membrane and soluble signaling proteins in the flagellar matrix. Here we employ a combination of genetic and mechanical approaches to purify intact flagella from the African trypanosome, Trypanosoma brucei, in its mammalian-infectious stage. We combined flagellum purification with affinity-purification of surface-exposed proteins to conduct independent proteomic analyses of the flagellum surface and matrix fractions. The proteins identified encompass a broad range of molecular functionalities, including many predicted to function in signaling. Immunofluorescence and RNA interference studies demonstrate flagellum localization and function for proteins identified and provide insight into mechanisms of flagellum attachment and motility. The flagellum surface proteome includes many T. brucei-specific proteins and is enriched for proteins up-regulated in the mammalian-infectious stage of the parasite life-cycle. The combined results indicate that the flagellum surface presents a diverse and dynamic host-parasite interface that is well-suited for host-parasite signaling. PMID:21685506

Semen proteomics and male infertility.

Science.gov (United States)

Jodar, Meritxell; Soler-Ventura, Ada; Oliva, Rafael

2017-06-06

Semen is a complex body fluid containing an admixture of spermatozoa suspended in secretions from the testes and epididymis which are mixed at the time of ejaculation with secretions from other accessory sex glands such as the prostate and seminal vesicles. High-throughput technologies have revealed that, contrary to the idea that sperm cells are simply a silent delivery vehicle of the male genome to the oocyte, the sperm cells in fact provide both a specific epigenetically marked DNA together with a complex population of proteins and RNAs crucial for embryogenesis. Similarly, -omic technologies have also enlightened that seminal fluid seems to play a much greater role than simply being a medium to carry the spermatozoa through the female reproductive tract. In the present review, we briefly overview the sperm cell biology, consider the key issues in sperm and seminal fluid sample preparation for high-throughput proteomic studies, describe the current state of the sperm and seminal fluid proteomes generated by high-throughput proteomic technologies and provide new insights into the potential communication between sperm and seminal fluid. In addition, comparative proteomic studies open a window to explore the potential pathogenic mechanisms of infertility and the discovery of potential biomarkers with clinical significance. The review updates the numerous proteomics studies performed on semen, including spermatozoa and seminal fluid. In addition, an integrative analysis of the testes, sperm and seminal fluid proteomes is also included providing insights into the molecular mechanisms that regulate the generation, maturation and transit of spermatozoa. Furthermore, the compilation of several differential proteomic studies focused on male infertility reveals potential pathways disturbed in specific subtypes of male infertility and points out towards future research directions in the field. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamic Safety Cases for Through-Life Safety Assurance

Science.gov (United States)

Denney, Ewen; Pai, Ganesh; Habli, Ibrahim

2015-01-01

We describe dynamic safety cases, a novel operationalization of the concept of through-life safety assurance, whose goal is to enable proactive safety management. Using an example from the aviation systems domain, we motivate our approach, its underlying principles, and a lifecycle. We then identify the key elements required to move towards a formalization of the associated framework.

Combinatorial hexapeptide ligand libraries (ProteoMiner): an innovative fractionation tool for differential quantitative clinical proteomics.

Science.gov (United States)

Hartwig, Sonja; Czibere, Akos; Kotzka, Jorg; Passlack, Waltraud; Haas, Rainer; Eckel, Jürgen; Lehr, Stefan

2009-07-01

Blood serum samples are the major source for clinical proteomics approaches, which aim to identify diagnostically relevant or treatment-response related proteins. But, the presence of very high-abundance proteins and the enormous dynamic range of protein distribution hinders whole serum analysis. An innovative tool to overcome these limitations, utilizes combinatorial hexapeptide ligand libraries (ProteoMiner). Here, we demonstrate that ProteoMiner can be used for comparative and quantitative analysis of complex proteomes. We spiked serum samples with increasing amounts (3 microg to 300 microg) of whole E. coli lysate, processed it with ProteoMiner and performed quantitative analyses of 2D-gels. We found, that the concentration of the spiked bacteria proteome, reflected by the maintained proportional spot intensities, was not altered by ProteoMiner treatment. Therefore, we conclude that the ProteoMiner technology can be used for quantitative analysis of low abundant proteins in complex biological samples.

Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Applied to Quantitative Proteomics of Bacillus subtilis

DEFF Research Database (Denmark)

Soufi, Boumediene; Kumar, C.; Gnad, F.

2010-01-01

We applied stable isotope labeling by amino acids in cell culture (SILAC) to large-scale quantitative proteomics analyses of the model bacterium Bacillus subtilis in two physiological conditions: growth on succinate and growth under phosphate starvation. Using a B. subtilis strain auxotrophic...... of the most comprehensive quantitative proteomics studies in bacteria, covering more than 75% of the B. subtilis genes expressed in the log phase of growth. Furthermore, we detect and quantify dynamics of 35 Ser/Thr/Tyr phosphorylation sites under growth on succinate, and 10 phosphorylation sites under...

Characterizing the Syphilis-Causing Treponema pallidum ssp. pallidum Proteome Using Complementary Mass Spectrometry.

Directory of Open Access Journals (Sweden)

Kara K Osbak

2016-09-01

Full Text Available The spirochete bacterium Treponema pallidum ssp. pallidum is the etiological agent of syphilis, a chronic multistage disease. Little is known about the global T. pallidum proteome, therefore mass spectrometry studies are needed to bring insights into pathogenicity and protein expression profiles during infection.To better understand the T. pallidum proteome profile during infection, we studied T. pallidum ssp. pallidum DAL-1 strain bacteria isolated from rabbits using complementary mass spectrometry techniques, including multidimensional peptide separation and protein identification via matrix-assisted laser desorption ionization-time of flight (MALDI-TOF/TOF and electrospray ionization (ESI-LTQ-Orbitrap tandem mass spectrometry. A total of 6033 peptides were detected, corresponding to 557 unique T. pallidum proteins at a high level of confidence, representing 54% of the predicted proteome. A previous gel-based T. pallidum MS proteome study detected 58 of these proteins. One hundred fourteen of the detected proteins were previously annotated as hypothetical or uncharacterized proteins; this is the first account of 106 of these proteins at the protein level. Detected proteins were characterized according to their predicted biological function and localization; half were allocated into a wide range of functional categories. Proteins annotated as potential membrane proteins and proteins with unclear functional annotations were subjected to an additional bioinformatics pipeline analysis to facilitate further characterization. A total of 116 potential membrane proteins were identified, of which 16 have evidence supporting outer membrane localization. We found 8/12 proteins related to the paralogous tpr gene family: TprB, TprC/D, TprE, TprG, TprH, TprI and TprJ. Protein abundance was semi-quantified using label-free spectral counting methods. A low correlation (r = 0.26 was found between previous microarray signal data and protein abundance.This is

Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models

International Nuclear Information System (INIS)

Rogers, Simon; Girolami, Mark; Kolch, Walter; Waters, Katrina M.; Liu, Tao; Thrall, Brian D.; Wiley, H. S.

2008-01-01

Modern transcriptomics and proteomics enable us to survey the expression of RNAs and proteins at large scales. While these data are usually generated and analyzed separately, there is an increasing interest in comparing and co-analyzing transcriptome and proteome expression data. A major open question is whether transcriptome and proteome expression is linked and how it is coordinated. Results: Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner. Our coupled mixture model defines a prior probability distribution over the component to which a protein profile should be assigned conditioned on which component the associated mRNA profile belongs to. By providing probabilistic assignments this approach sits between the two extremes of concatenating the data on the assumption that mRNA and protein clusters would have a one-to-one relationship, and independent clustering where the mRNA profile provides no information on the protein profile and vice-versa. We apply this approach to a large dataset of quantitative transcriptomic and proteomic expression data obtained from a human breast epithelial cell line (HMEC) stimulated by epidermal growth factor (EGF) over a series of timepoints corresponding to one cell cycle. The results reveal a complex relationship between transcriptome and proteome with most mRNA clusters linked to at least two protein clusters, and vice versa. A more detailed analysis incorporating information on gene function from the gene ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular machines, such as the ribosome, cell adhesion complexes and the TCP-1 chaperonin involved in protein folding. Conclusions: The dynamic regulation of the transcriptome and proteome in mammalian cells in response to an acute mitogenic stimulus appears largely independent with very little

Proteomic approaches in brain research and neuropharmacology.

Science.gov (United States)

Vercauteren, Freya G G; Bergeron, John J M; Vandesande, Frans; Arckens, Lut; Quirion, Rémi

2004-10-01

Numerous applications of genomic technologies have enabled the assembly of unprecedented inventories of genes, expressed in cells under specific physiological and pathophysiological conditions. Complementing the valuable information generated through functional genomics with the integrative knowledge of protein expression and function should enable the development of more efficient diagnostic tools and therapeutic agents. Proteomic analyses are particularly suitable to elucidate posttranslational modifications, expression levels and protein-protein interactions of thousands of proteins at a time. In this review, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) investigations of brain tissues in neurodegenerative diseases such as Alzheimer's disease, Down syndrome and schizophrenia, and the construction of 2D-PAGE proteome maps of the brain are discussed. The role of the Human Proteome Organization (HUPO) as an international coordinating organization for proteomic efforts, as well as challenges for proteomic technologies and data analysis are also addressed. It is expected that the use of proteomic strategies will have significant impact in neuropharmacology over the coming decade.

Proteomic landscape in Central and Eastern Europe: the 9th Central and Eastern European Proteomic Conference, Poznan, Poland

Czech Academy of Sciences Publication Activity Database

Gadher, S. J.; Marczak, L.; Luczak, M.; Stobiecki, M.; Widlak, P.; Kovářová, Hana

2016-01-01

Roč. 13, č. 1 (2016), s. 5-7 ISSN 1478-9450. [Central and Eastern European Proteomic Conference (CEEPC) /9./. Poznaň, 15.06.2015-18.06.2015] Institutional support: RVO:67985904 Keywords : Central and Eastern Proteomic Conference * proteomics * mass spectrometry imaging Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.849, year: 2016

Investigation concerning the relative formation rate and half-life time of short-lived nuclides with a fast conveyor tube system

International Nuclear Information System (INIS)

Kreiner, H.J.

1976-01-01

Since the installation of the 'Ultrafast Rabbit System' at the FRN in end of 1974, some research was started concerning the possibility of neutron activation analysis of short-lived nuclides (0.02 1/2 < 1 s) and measurements of short-lived fission products of U-235 and Pu-239. One of the results of the investigations is a more exact gamma-energy determination of the 0.8 s Cl-38m with 671.33 keV. In NAA it was possible to reach a sensitivity for lead and boron near 2 μg per sample respectively 10 ppm. In measurements of light fission products 0.1 - 8s after a pulse irradiation some differences of the relative formation rate and half-life in the region of A approximately 100 were found in comparison to literature. For example a strong build-up could be seen measuring the gamma-energy of 276.1 keV that belongs to Nb-101. Therefore we suppose the existence of an isomeric state of Nb-101. In comparison to our own results of yield ratio of the Pu- and U-fission products a good agreement with known data was found. Furthermore the measuring method gives the possibility of coordination of unknown gamma-lines to nuclides using the rate of formation, the half-life, the yield ratio between U and Pu and the build-up factor. That could be verified in some cases, e.g. Nb-103 and Sr-96. (author)

Establishing Substantial Equivalence: Proteomics

Science.gov (United States)

Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle.

Science.gov (United States)

Shock, Jennifer L; Fischer, Kael F; DeRisi, Joseph L

2007-01-01

The rate of mRNA decay is an essential element of post-transcriptional regulation in all organisms. Previously, studies in several organisms found that the specific half-life of each mRNA is precisely related to its physiologic role, and plays an important role in determining levels of gene expression. We used a genome-wide approach to characterize mRNA decay in Plasmodium falciparum. We found that, globally, rates of mRNA decay increase dramatically during the asexual intra-erythrocytic developmental cycle. During the ring stage of the cycle, the average mRNA half-life was 9.5 min, but this was extended to an average of 65 min during the late schizont stage of development. Thus, a major determinant of mRNA decay rate appears to be linked to the stage of intra-erythrocytic development. Furthermore, we found specific variations in decay patterns superimposed upon the dominant trend of progressive half-life lengthening. These variations in decay pattern were frequently enriched for genes with specific cellular functions or processes. Elucidation of Plasmodium mRNA decay rates provides a key element for deciphering mechanisms of genetic control in this parasite, by complementing and extending previous mRNA abundance studies. Our results indicate that progressive stage-dependent decreases in mRNA decay rate function are a major determinant of mRNA accumulation during the schizont stage of intra-erythrocytic development. This type of genome-wide change in mRNA decay rate has not been observed in any other organism to date, and indicates that post-transcriptional regulation may be the dominant mechanism of gene regulation in P. falciparum.

Topology and Oligomerization of Mono- and Oligomeric Proteins Regulate Their Half-Lives in the Cell.

Science.gov (United States)

Mallik, Saurav; Kundu, Sudip

2018-06-05

To find additional structural constraints (besides disordered segments) that regulate protein half-life in the cell, we herein assess the influence of native topology of monomeric and sequestration of oligomeric proteins into multimeric complexes in yeast, human, and mouse. Native topology acts as a molecular marker of globular protein's mechanical resistance and consequently captures their half-life variations on genome scale. Sequestration into multimeric complexes elongates oligomeric protein half-life in the cell, presumably by burying ubiquitinoylation sites and disordered segments required for proteasomal recognition. The latter effect is stronger for proteins associated with multiple complexes and for those binding early during complex self-assembly, including proteins that oligomerize with large proportions of surface buried. After gene duplication, diversification of topology and sequestration into non-identical sets of complexes alter half-lives of paralogous proteins during the course of evolution. Thus, native topology and sequestration into multimeric complexes reflect designing principles of proteins to regulate their half-lives. Copyright © 2018 Elsevier Ltd. All rights reserved.

Proteome identification of the silkworm middle silk gland

Directory of Open Access Journals (Sweden)

Jian-ying Li

2016-03-01

Full Text Available To investigate the functional differentiation among the anterior (A, middle (M, and posterior (P regions of silkworm middle silk gland (MSG, their proteomes were characterized by shotgun LC–MS/MS analysis with a LTQ-Orbitrap mass spectrometer. To get better proteome identification and quantification, triplicate replicates of mass spectrometry analysis were performed for each sample. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Vizcaíno et al., 2014 [1] via the PRIDE partner repository (Vizcaino, 2013 [2] with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD003371. The peptide identifications that were further processed by PeptideProphet program in Trans-Proteomic Pipeline (TPP after database search with Mascot software were also available in .XML format files. Data presented here are related to a research article published in Journal of Proteomics by Li et al. (2015 [3]. Keywords: Bombyx mori, Middle silk gland, Silk protein synthesis, Shotgun proteomics, Label-free